CAMPARI Activity
Software for molecular simulations and trajectory analysis
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Activity for CAMPARI
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CAMPARI released /campari/campari_v5_04192024.zip
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Andreas Vitalis created a blog post
Version 5 released!
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Wenwen (Velurön) Leng modified a comment on discussion Help
Well done and many thanks!
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Hi, I am trying to install CAMPARI by the online tutorial instructions, but finally get the error: /home/veluron/snap/software/campari/source/allocate.f90:4099:2: 4099 | #else | 1~~~ Fatal Error: fftw3_SUN.f03: No such file or directory compilation terminated. make: *** [Makefile:184: /home/veluron/snap/software/campari/lib/x86_64/allocate.o] Error 1 I also tried to solve through Google, but there is nothing about that. I just use the Partially Automatic Installation for i have installed the basic...
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Hi Andreas, Thanks for your suggestions. I clean them all and restart again from the begining. But still to find: *** No rule to make target ~/libxdrf.a'. I remember that the procedure of automatic installation will set XDR lib. So I am not sure what happened. In any cases, please find my attached log flies. https://upload.cc/i1/2024/01/12/oeg0vE.png Thanks in advance. Wenwen (Velurön) Leng
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Hi, the mention of the file fftw3_SUN.f03 implies that you are trying to use the Oracle (Sun) compiler. Is this correct? If no: You are accidentally passing "-DORACLE_FORTRAN" in your Makefile (just grep for this string). I don't know where that would be coming from, though. Removing it from the Makefile and recompiling everything should fix it (make clean; make all install). If yes, you have a few options: 1. Use the GNU compilers instead (rerun configure, and recompile) 2. Install FFTW3 using the...
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Hi, I am trying to install CAMPARI by the online tutorial instructions, but finally get the error: /home/veluron/snap/software/campari/source/allocate.f90:4099:2: 4099 | #else | 1~~~ Fatal Error: fftw3_SUN.f03: No such file or directory compilation terminated. make: *** [Makefile:184: /home/veluron/snap/software/campari/lib/x86_64/allocate.o] Error 1 I also tried to solve through Google, but there is nothing about that. I just use the Partially Automatic Installation for i have installed the basic...
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Hi Irem, harmonic angular restraints on arbitrary atoms are not supported because they create force discontinuities when the angle approaches 180 deg. , which would take some extra mechanisms to protect from. This is not an issue for standard topological bonds that contain no angles near 180 deg. Unsupported residues or small molecules can contain sp carbons of course, and I don't recall from top of my head what happens to those in Cartesian dynamics. It's probably possible to mimic an angle restraint...
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Irem posted a comment on discussion Help
Hello all, I need to setup a system with harmonic restraints, and I'm running into problems. I have two general questions: 1- Is it possible to set up harmonic angular restraints? As far as I can tell from the documentation, the answer seems to be no, but I wanted to double check. 2- When I set up a simulation with harmonic distance restraints using FMCSC_SC_DREST, is there a way to check that the system is in fact applying them? Is there a harmonic energy calculation somewhere that the simulation...
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I am reposting the message I sent you for reference here: The "make campari" error is, as you diagnosed, because there is no file called "Makefile" by default. The second error is probably because you have not created the lib/bin subfolders beforehand. To avoid linking errors downstream, I would follow the official instructions (which also contain a sample Makefile.local for Linux systems with Gnu compilers). I am going to assume for simplicity that you work in the folder /software/campari With configure:...
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Hi, apologies for the extraordinary delay. Almost certainly you solved this but for reference: Indeed, the XDR library has issues with Ubuntu 22 and newer. Some components of RPC were migrated out, which leads to the new requirements to: 1) Install the extra package (as you write) 2) Add "-I/usr/include/ntirpc" to the C compiler flags (as you write) 3) Add "-ltirpc" to the linker flags Cheers, Andreas
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I am sorry for the inordinate delay, but in case this question still matters to you or others: I believe the error is because there is a limit parameter that is not correctly set. Note that this feature is largely obsolete (as the documentation states). I can reproduce a seg-fault if in "mod_grid.f90" I have: integer MAXGRID parameter (MAXGRID=900) But it goes away if I recompile with: integer MAXGRID parameter (MAXGRID=1300) The grids are simply setting up a biased sampler that is meant to prevent...
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srinivasan posted a comment on discussion Help
Hi, I am trying to install CAMPARI to run the md simulation using the absinth model for the biomolecular condensates and facing issues during the installation process. I tried following the Github page of Alex for installation where during Make campri i get the error make campari make: *** No rule to make target 'campari'. Stop. I also tried using the make -f MakeFile.manual campari but ended up with Fatal error: can't create ../lib/x86_64/libxdrf.o: No such file or directory make[1]: *** [Makefile:53:...
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Dietrich Trümbach posted a comment on discussion Help
Hello, I tried to run a simulation with PIVOTMODE 2 and the GRIDDIR $CAMPARIHOME/data/grids. After that I got a segmentation fault (see part of the log file below). Does anyone know what that means and how to prevent the error? I also attached the key file with the parameter settings. Background is to model the unfolded protein state by applying Flory Random Coil (FRC) simulations (Holehouse et al. 2015). Or does anyone know how to simulate the unfolded state without using the grids folder (because...
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Lisa Tuttle posted a comment on discussion Help
Hello, I'm attempting to compile Campari v4 on Ubuntu 22.04 using the Gnu compilers. I have made it most of the way through the process but am getting XDR related errors at the linking step. # linking hopefully as well (see above note, true here due to target location!) campari: ${LINKDEPS1} ${FF} $(LFLAGS) -o ${BIN_DIR}/${ARCH}/campari ${LIB_DIR}/${ARCH}/chainsaw.o ${LIB_DIR}/${ARCH}/lcampari.a ${EXTRA_LIBS} which executes as gfortran -O3 -o /usr/software/Campari/bin/Gnu/campari /usr/software/Campari/lib/Gnu/chainsaw.o...
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Hi, I was wondering if you wrote down some notes about how you managed to get the installation to work on macos and would be willing to share? (It's fine that it's slower -- I just need to use it to set up systems and will run the actual simulations on the cluster.)
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Hi, I'm trying to install CAMPARI on macOS 11.5.2. I have gcc, gfortran, and I managed to install some of the required libraries with homebrew. After pointing the configure script to the right location for automake/install-sh, I was able to run the configure script. However, running make afterwards results in the following error: ➜ source make all install gfortran -DDISABLE_FLOAT -DLINK_LAPACK -DLINK_XDR -DLINK_FFTW -O3 -march=native -funroll-loops -I/usr/local/include -c -cpp -fall-intrinsics -ffpe-trap=invalid,zero...
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Hi Feng, I am sorry I completely missed this. "install" is part of coreutils, so should pretty much always be there on Linux. It might be that the lines right before failed due to permissions. This could happen if you used the route through Makefile.manual and didn't redefine DESTDIRBIN and DESTDIRLIB there. The documentation doesn't specifically cover this case (running "make install" in the manual route). If this happens with the configure script, it should throw an error earlier. We'll look into...
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Feng Yu posted a comment on discussion Help
Hi I have installed all necessary library accroding to the tutrorial. But when I install using semi-auto method, I got an error on this line. install -v ${LIB_DIR}/${ARCH}/lib*a ${DESTDIRLIB} I succecefully installed the package after comment out this line. I want to know whether this is a typo or not. Best Feng Yu This line is in the following section of the Makefile. install: if [ ! -d ${DESTDIRBIN} ]; then ${MKDIR} -pv ${DESTDIRBIN}; fi if [ ! -d ${DESTDIRLIB} ]; then ${MKDIR} -pv ${DESTDIRLIB};...
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Hi Jihye, not sure I can correlate the keywords exactly with your question (FMCSC_XYZOUT, FMCSC_NRSTEPS and FMCSC_EQUIL give me 10M production steps and 500 written snapshots for a single run) but the problem might be that some specific amino acids, specifically SER/THR/TYR, fail. I am assuming you are running blocked amino acids (aka , dipeptides) so something like ACE-SER-NME. Crashes might happen because you didn't use FMCSC_FUDGE_DYN 1 but a time step of 4fs. The CCOH-dihedral angle is a very...
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Jihye Park posted a comment on discussion Help
Hello, I'm a graduate student in Korea and I got a problem while testing on implicit solvent molecular dynamics simulations of blocked amino acids with different initial structures. The problem is that even though I used the same key files for all the simulations, some of them do not end at the specified time step. To be specific, some of them end at 680 timesteps while the others end at 1000 timesteps normally. The only difference is the initial structure, so I wonder how can I resolve this problem....
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Hi Yifan, this issue is an odd one. We have recently gained access to our latest HPC architecture, which have 2x64-core AMD Epyc processors on them, and I did not encounter any obvious problems. When you try V4 with gfortran, make sure to disable the Fortran08 MPI module (pass "-DDISABLE_MPIF08"). There is a currently unresolved bug in gfortran with the module, at least with the MPICH-based module I have available on my HPC system (note that V3 is not using the Fortran08 MPI module, so this problem...
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Yifan Zhang posted a comment on discussion Help
Hi Andreas, Thank you so much for your advice! I have tried to install the code again without FFTW but the same problem is still recurring. The compiler I used was gcc. I managed to finish the simulation run by using the restart files whenever the simulation has stopped. I plan to try out the newly released v4 and I'll let you know if that helped! Another question about the simulation set-up: I have been running duplicate simulations of ~50,000,000 steps for my peptide of 50 residues and taking snapshot...
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Version 4 released!
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Hi Yifan, that is a challenging question to answer since I don't have access to such a machine. Generally speaking, you can completely remove PME form the code by simply not linking to FFTW during compilation (so do not specify -DLINK_FFTW). I don't know what exact simualtions you run, but using PME would only be relevant for explicit solvent simulations. I think there is only one tutorial that actually uses PME. Whenever keyword FMCSC_LREL_MD is not 2, no Ewald routines are used in any way. If you...
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Hi guys, I'm new to campari, and I kept running into odd terminations when I tried to follow the tutorial or to do my own project. The job would run fine for several hours and then stop at some point with no warnings showing up in the log. No matter how large the job is, the stop would always occur at ~2h into the simulation. The system is a simple IDP monomer. I'm using the 96-CPU AWS EC2 machines that I always use for my other MD projects. The problem might be AWS EC2 specific because I also had...
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Sorry about the delay: At the moment, you would have to use it as an unsupported. Charges you could get from CHARMM via CgenFF or by analogy. Depending on your plans, though, it could be rather tricky to parameterize. The energy scales for true divalent ions get very large, which also very negatively impacts sampling (effective time scales). In ABSINTH (and in line with most force fields), we have been avoiding divalent ions because of this. That said, I know that Martin Fossat in the Pappu lab was...
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Siddharth Marwaha modified a comment on discussion Help
As per the documentation, the TPO residue is the hydrogen phosphate ester of threonine, and accordingly carries a -1 charge. However, if I wanted a deprotonated version of this (with a -2 charge), would that be possibe? And if so, which force field would be best to utilize, if there is one?
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As per the documentation, the TPO residue is the hydrogen phosphate ester of threonine, and accordingly carries a -1 charge. However, if i wanted a deprotonated version of this (with a -2 charge), would that be possibe? And if so, which force field would be best to utilize, if there is one?
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Gianluca Interlandi posted a comment on discussion Help
Hi Andreas, Thanks for your reply. 3) I'll set something up, hopefully this week. 3gxb is a dimer in the PDB, but I assume you want the monomer? The PDB file that I uploaded here: http://gianluca.today/Files/Campari/ is a monomer. If you want to use directly the PDB file deposited with PDB code 3GXB, then I would use chain A. Best, Gianluca Gianluca Interlandi, PhD gianluca@u.washington.edu +1 (206) 685 4435 http://gianluca.today/ Research Assistant Professor at the Department of Bioengineering at...
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Hi Gianluca, sorry for the delay: 1) Citations: no, not explicitly for docking. The polyQ work I mentioned is here: https://doi.org/10.1016/j.jmb.2008.09.026 https://doi.org/10.1016/j.bpj.2009.05.003 The other works were specifically interested in characterizing or predicting interfaces but rather simulated known complexes. Marco Bacci has done the most with that on our end recently. 2) The offset is on a parameter that is the reference free energy of solvation for a solvation group. In ABSINTH,...
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Hi Andreas, Thanks for your answers. If you don't mind, I have more questions: 1) Do you have some citations about your protein docking studies with CAMPARI? That would be helpful. 2) What distance does -30kcal/mol per group roughly correspond to? Is it similar to CHARMM22 10-12 LJ cutoff with switching? 3) I would be interested in synergizing. But, I would like to get first an estimate of the performace. For example, to do rigid-body docking of the following two globular proteins. How long would...
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Hi Gianluca, 1) We have simulated several protein complexes in the past. In the earliest days, we were interested in the binding affinity of globules of polyQ. That is a case where we did a comparison of affinity in a rigid approximation vs flexible, and we found that flexibility increases affinity (to be expected, though, as the interfaces were not "optimized" for binding). So both (rigid/flexible) are possible. Most other protein complexes were treated with some amount of flexibility. Marco may...
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Dear CAMPARI developers and users, I have a few questions concerning CAMPARI/ABSINTH: 1) Has CAMPARI ever been used to model the complex of two globular protein domains by treating them as rigid bodies? 2) In the ABSINTH paper (2009) I read that "it is designed primarily for simulating conformational equilibria and oligomerization reactions of intrinsically disordered proteins in aqueous solutions". Is there any evidence , or arguments in favor, that ABSINTH would correctly describe the complex between...
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Hi Anne, first apologies for the delay. Cyclic peptides are a tricky issue since most of CAMPARI's functionality (the MC part in particular) is built on the logic that torsion angles are the degrees of freedom. With a cyclic constraint, every backbone move in torsional space has to be of a concerted rotation type. There are two possible solutions: o You can work in Cartesian space (see FMCSC_CARTINT) and treat the molecule has a single, unsupported "residue". This requires a lot of patches should...
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Hi Chris, this is way outdated, I apologize. For restarting runs, look at FMCSC_RESTART, for analyzing data on the fly, just analyze the trajectories being written (this is usually safe as read access does not conflict with them being open for writing) using FMCSC_PDBANALYZE . If you want more control have a look at FMCSC_FRAMESFILE. Cheers, Andreas
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Anne Kiirikki posted a comment on discussion Help
Is it possible to do MC and MD simulations on a cyclic amino acid chain with CAMPARI? I have a disordered protein molecule where the N and C termini are joined by a bond. How can I pass the information about this bond in CAMPARI?
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Taehyung Chris Lee posted a comment on discussion Help
Dear CAMPARI users, Is it possible to continue a job after it has been interrupted(ie. Power outage, etc.)? Additionally, is it possible to analyze the data in the middle of a run, to make sure it is running properly? Thank you! Taehyung Chris Lee Sent from my iPhone
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Dear Andreas, Thank you so much! I could build CAMPARI with the fixes that you suggested! (I needed to make couple more changes for reference: curl was somehow having hard time to be found so I gave the directory for it in the Makefile.local. Also, "override-limits" in Makefile was needed to be changed to "qoverride-limits" for my compiler. I am using complier included in Parallel Studio XE 2019.) Just one last question on installation: Is it necessary to delete all compiled module files, and libraries...
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Hi Chris, you've got several issues. First, in Makefile, you should change: COMPDEFAULTS=${INTELDEFAULTS} from COMPDEFAULTS=${GNUDEFAULTS} Second, you need to worry about where you are going to get your dependencies from, in particular NetCDF. For example, if you use only system packages, your Makefile.local would include lines like these: EXTRA_LIBS=-lnetcdff -lnetcdf -lfftw3_threads -lfftw3 -llapack MPIEXTRA_LIBS=-lnetcdff -lnetcdf -lfftw3_threads -lfftw3 -llapack HSLEXTRALIBS=-lblas However, for...
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Hello Andreas, Thank you for the help. I was thinking, is it possibly due to the ifort? I am using 64-bit compiler but maybe I should use 32-bit? Here are some lines from command window before the Error 1: ifort -DLINK_NETCDF -DLINK_XDR -DLINK_LAPACK -DDISABLE_ERFTAB -DDISABLE_FLOAT -DLINK_FFTW -DLINK_HSL -march=native -funroll-loops -c -cpp -O3 -fall-intrinsics -ffpe-trap=invalid,zero -std=f2008 -fdefault-real-8 -fdefault-double-8 -qopenmp -I/home/labuser/campari/lib/Intel/threads -DENABLE_THREADS...
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Hello Andreas, Thank you for the help. I was thinking, is it possibly due to the ifort? I am using 64-bit compiler but maybe I should use 32-bit? Here are some lines of command window befre that: ifort -DLINK_NETCDF -DLINK_XDR -DLINK_LAPACK -DDISABLE_ERFTAB -DDISABLE_FLOAT -DLINK_FFTW -DLINK_HSL -march=native -funroll-loops -c -cpp -O3 -fall-intrinsics -ffpe-trap=invalid,zero -std=f2008 -fdefault-real-8 -fdefault-double-8 -qopenmp -I/home/labuser/campari/lib/Intel/threads -DENABLE_THREADS /home/labuser/campari/source/mod_ncdm.f90...
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Hi, is there anything more to this error? What were the few lines before? Please do: "make clean", the "./make_dependencies.sh ." and then "make campari_threads" or "make campari". Your architecture is definitely not a problem. We use Intel compilers on Ubuntu ourselves. I should be able to help you more with that information available. Cheers, Andreas
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Dear Campari users, Sorry I am new to this so please bear with me, I am encountering issue with installation for Campari. My "make campari" command is keep getting aborted with message saying: "compilation aborted for /home/labuser/campari/source/clustering.f90 (code 1) make: *** [/home/labuser/campari/lib/Intel/threads/clustering.o] Error 1" May I ask you what might be wrong? I am using ubuntu 14.04 and the CPU is Intel® Xeon. I am using Intel Fortran Compiler. Thank you in advance for your hel...
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Hi Steffen, sorry I overlooked this. Out of curiosity: what type of benchmark were you looking at for the speed comparison? OpenMP/no OpenMP? It's rare that on a standard CPU, you would get such large differences. One reason could be that gfortran failed to pull the right instructions sets through "march=native". I don't have a Mac lying around, so I cannot test easily.
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Steffen Graether posted a comment on discussion Help
After a day's rest I figured out how to correctly link the libraries. Unfortunately it seems all for naught, since oddly the Mac Pro is ~5x slower than my linux workstation.
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Hi, I'm trying to install Campari v3 on MacOS (my Makefile.local is attached). I've gotten mostly there, but after spending quite some time troublshooting, I can't get past the follwing errors : gfortran -O3 -o /usr/local/campari/bin/Intel/campari /usr/local/campari/lib/Intel/chainsaw.o /usr/local/campari/lib/Intel/lcampari.a /usr/local/Cellar/fftw/3.3.8/lib/libfftw3.a /usr/local/Cellar/fftw/3.3.8/lib/libfftw3_threads.a -lblas -llapack /usr/local/Cellar/netcdf/4.6.1_4/lib/libnetcdff.a /usr/local/Cellar/netcdf/4.6.1_4/lib/libnetcdf.a...
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I would probably keep the neutralizing ones as excess, which is more likely to be similar to reality (ionic atmospheres and all).
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Jonathan Huihui posted a comment on discussion Help
Thank you for the quick reply! Just one more question on this topic - Since the input sequence file needs to be net neutral, would it be best practice to (following your example): 1) Neutralize the protein chain with counterions (say 6 NA+) 2) Add the remaining required ions of that same charge (41-42 NA+) 3) Add the same amount of opposite charge as were added in step 2 (41-42 CL-) Thanks, Jonathan
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Hi Jonathan, I hope this is answering your question: The sequence file always has to be explicit, i.e.,, all residues, which includes ions, have to be listed, one per line. So it depends on your volume and the numbers you put. Keep in mind that in a droplet the formal volume and the actual volume are not exactly the same because the wall is soft. E.g,, 150mM in a 50A radius droplet using the formal volume is between 47 and 48 cat- and anions each. There is currently no way to shorten the sequence...
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I have been looking through the documentation and I haven't been able to find out how to run simulations with a solvent salt concentration (using CAMPARI v2). i.e. I am looking to run simulations at different salt concentrations: 0, 10, 50, 100mM, etc. If I could get some guidance on how to do this I would greatly appreciate it!
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Hi Dillion, Did you get N_000.log or N_001.log? Once CAMPARI starts, almost all errors are printed there. So if you have a problem with the key-file, CAMPARI would throw an error and then trigger MPI_ABORT. If there aren't too many MPI ranks I usually do st like: tail N_*.log The error usually shows up only in the rank to first encounter it (and triggers the destruction of the MPI universe), which can be random. If that is not the problem, let me know! Andreas
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Dillion Fox posted a comment on discussion Help
Ah ha! That file does indeed exist, and the issue was spelled out very clearly in it. Thank you very much for your help.
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Hi Dillion, Did you get N_000.log or N_001.log? Once CAMPARI starts, almost all errors are printed there. So if you have a problem with the key-file, CAMPARI would throw and error and than trigger MPI_ABORT. If there aren't too many MPI ranks I usually do st like: tail N_*.log The error usually shows up only in the rank to first encounter it (and triggers the destruction of the MPI universe), which can be random. If that is not the problem, let me know! Andreas
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I installed CAMPARI 3 on a CRAY XK7 platform with Intel compilers and linked it to fresh installations of FFTW, NetCDF, LAPACK, BLAS, CMAKE, etc. The installation appeared to be successful, but when I try to run the code with mpirun I get an MPI_ABORT error. For example, when trying to run test.key (which worked on a different machine without MPI): mpirun -n 2 campari_mpi_threads -k test.key Using system environment-defined value for the number of threads per MPI proces Using system environment-defined...
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Tere posted a comment on discussion Help
Thanks so much Dr. Andreas The message error was the next: gfortran -DISABLE_FLOAT -DLINK_XDR -DLINK_FFTW -DLINK_NETCDF -I/home/tere/campari/local_libs/local/include -I/home/tere/Desktop/campari/lib/x86_64/ -c -cpp -O3 -fall-intrinsics -ffpe-trap=invalid,zero -std=f2008 -fdefault-real-8 -fdefault-double-8 -I/home/tere/Desktop/campari/lib/x86_64 /home/tere/Desktop/campari/source/getkey.f90 -o /home/tere/Desktop/campari/lib/x86_64/getkey.o gfortran -DISABLE_FLOAT -DLINK_XDR -DLINK_FFTW -DLINK_NETCDF...
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Hi everyone, Im trying to follow the tutorial 1 with the next sequence : ACE ALA ALA ALA ALA ALA ALA SER VAL VAL VAL PRO THR PRO THR TYR PRO LYS TYR PRO TRP ASN ASN PHE HID MET SER PRO TYR THR ALA GLU PHE TYR ARG THR ILE ASN GLN GLN GLY HID GLN ILE LEU PRO NME END And all the parameters identical in the tutorial1.key , and I had this message: Molecule type 1 has 47 residues and a mass of 5105.8040 D. The first example molecule is # 1 (residues 1- 47). There are 1 molecules of this type. Polymer analysis...
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Hi Maria, in general, yes. If you can afford it, you could also set up some comparison runs with abs3.4_charmm36.prm. These parameters are meant to correct some weaknesses identified over the years with the abs3.2... parameters for free energies of solvation of inorganic ions and selected Lennard-Jones parameters. If you run into unexpected behavior, please let us know! Andreas
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Mariya Shadrina posted a comment on discussion Help
Hi Andreas, I am planning to do similar simulations as Steffen (comparison the Rg of unphosphorylated, phosphorylated and pseudo-phosphorylated protein in an implicit solvent simulation). I am wondering if abs3.2_charmm36.prm is the best option to do it among all CHARMM parameter files available in CAMPARI? Thank you! Maria.
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Marco Bacci posted a comment on discussion Help
Dear Maria, it seems to me that you are compiling the code on a machine and then you run it on a different one, which does not support AVX instructions but only SSE4.2. I suggest to compile your code forcing the instruction set to SSE4.2. You can do this by changing the entries: -axAVX -xAVX in your makefile local with: -axSSE4.2 -xSSE4.2. Hope that helps! Let us know. Cheers,
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Dear Marco, I have loaded the following modules and the compilation finished with no errors. 1) intel-compilers/12.0.4.191 2) netcdf/4.1.3 3) hdf5/1.8.9-intel 4) gcc/4.8.1 5) zlib/1.2.8 6) curl/7.54.0 Campari is created in the bin folder but it does not work. I get "Fatal Error: This program was not built to run in your system. Please verify that both the operating system and the processor support Intel(R) AVX." I have tried both ARCH=Intel and ARCH=x86_64 with the same result. I did not have the...
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Hi Tere, I am still not entirely sure what the error message I am supposed to help you with is. In general, I agree of course - I will see if anyone has a box with a CentOS 6.9 installation around. Once I have done so, I'll get back to you. Cheers, Andreas
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Hi Dr. Vitalis, I 've tried your recommendations in centos 6.9 , but it still without compiler. So, I have installed Ubuntu, and installed campari without any problem. I will be working with this architecture, but it will be great find a solution in centos for this problem. Thanks a lot for your support.
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Hi all, Marco and I have updated the web docu to be more specific about both HSL and NetCDF: http://campari.sourceforge.net/V3/install.html http://campari.sourceforge.net/V3/download.html Unfortunately the web docu is still very slow at the time of writing, which I assume is due to the data center migration of SF: https://twitter.com/sfnet_ops Cheers, Andreas
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Dear Maria, I think the problem is that you are linking the NetCDF statically. In order to do this it is required to specify extra links. I believe you should add the following flags: -lhdf5 -lhdf5_hl -lcurl -lz on the EXTRA_LIBS line of your make file, assuming you have system-wise installations of hdf5, zlib and curl libraries. I retrieve this information from here: https://www.unidata.ucar.edu/software/netcdf/docs/building_netcdf_fortran.html under the section " Building with static libraries"...
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Dear Marco, Thank you for the guidelines! Yes, it seems I have passed the HSL library. The next error is related to NetCDF. Not sure what is wrong alhough. Can I use the NetCDF-4.1.3? The end of my output looks like: /home/apps/Logiciels/netcdf-4.1.3/lib/libnetcdf.a(libnetcdf4_la-nc4type.o): In function `NC4_inq_type_equal': /home/rqchpbib/belandmi/netcdf-4.1.3/libsrc4/nc4type.c:77: undefined reference to `H5Tequal' /home/apps/Logiciels/netcdf-4.1.3/lib/libnetcdf.a(liboc_la-curlfunctions.o): In function...
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Dear Maria, I retested the installation on my machine this morning (Ubuntu 14.04). I believe that your error is due to file names that are not in compliance with the makefile. This is actually not well explained in our documentation. There are duplicated file names in the HSL routines, and it is necessary to rename them. I will update the documentation as soon as possible thanks to your feedback. Here are the steps that one has to take to also compile HSL routines during the compilation of CAMPARI....
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Dear Marco, it seems that a compiler passed ma48_sdeps90.f90 and ma48_ddeps90.f90 with no error but it complains now about hsl_ma48s.f90. Do you have any idea about what does it mean? Please see the error below. /home/campari/source/hsl/hsl_ma48s.f90(18): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [HSL_ZB01_SINGLE] use hsl_zb01_single, zb01_real_info => zb01_info -------^ /home/campari/source/hsl/hsl_ma48s.f90(19): error #7002: Error in opening the compiled module...
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Dear Maria, to the best of my knowledge you should be able to find ma48_sdeps90.f90 and ma48_ddeps90.f90 when you download HSL_ZD11 from http://www.hsl.rl.ac.uk/catalogue/ Similarly, you should find ma48_sdeps.f and ma48_sdeps.f from MC71 (same link as above). I hope this helps. Please, let us know if you encounter additional problems. Best,
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I think you had " -std=f2008" before, so can you also repost the error you get with that? The current error is due to INT64 being a 2008 feature. One thing you can try in addition is to pass "-DORACLE_FORTRAN" just for the compilation of graph_algorithms.f90 and thread_utils.f90. In other words, try this: gfortran -DORACLE_FORTRAN -DDISABLE_FLOAT -DLINK_XDR -DLINK_FFTW -DLINK_NETCDF -I/data2/teresa/campari/local_libs/local/include -I/data2/teresa/campari_abs/lib/x86_64/ -c -cpp -O3 -fall-intrinsics...
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Hello, I have downloded the ma48-2.2.0 library but there is no ma48_ddeps90.f90, ma48_ddeps.f, ma48_sdeps90.f90, ma48_sdeps.f files that CAMPARI requires. Only ddeps.f, sdeps.f, ma48d.f, ma48s.f. Could you tell me please where can I find the required files? Thank you! Best regards, Maria.
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Hi friends, Im trying to install campari version 3 in a Centos System, but when I try compiler (make campari), I have this error message. Sincerily, I don't know fortran and I was searching something about it and I dont have idea how resolve it. Any could help me or guide me about this point? Thanks so much [teresa@odin source]$ make campari gfortran -DDISABLE_FLOAT -DLINK_XDR -DLINK_FFTW -DLINK_NETCDF -I/data2/teresa/campari/local_libs/local/include -I/data2/teresa/campari_abs/lib/x86_64/ -c -cpp...
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Hi Andreas, Yes, that answers my question. The reason I was asking is that my phosphorylated form of our protein was extended compared to the wild-type protein, which somewhat surprised me because the pseudo-phosphorylated form showed some compaction. I thought maybe the extension was due to not neutralizing the SEP properly, causing some increased repulsion. Though I have found another problem that may have caused it. I will know in a few days. Many thanks, Steffen
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Hi Steffen, SEP is -1. All phosphorylated residues are in what is probably the most populated species, i.e., the hydrogenphosphate ester (-). I wouldn't recommend trying to simulate the naked terminal phopshate (2-) in any case (not that that is supported at the moment). I am not entirely sure that answers your question, though. Andreas
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Hi Andreas, In the end I decided to use the CHARMM36 parameter set instead because it would be easier for me and give me more confidence of a correct simulation. I treated SEP residues as -2 charge, but when I run campari it complains about the system having a 5 unit charge. Am I missing something simple here? Regards, Steffen
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Well, two things come to mind: 1) You may want to consider keeping the backbone charges from OPLS-AA/L. In both CHARMM and OPLS, the NHCHCO scaffold is always net neutral and does not vary with sidechain. For the rest, you'll just need to define new charge types. The phosphate groups are parameterized to be singly negatively charged, so they carry one OH. CAMPARI will complain if the charges do not add up correctly, so this part is usually relatively easy to debug. 2) Bonded paramteters are needed...
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Hi Andreas, Ah okay that makes sense now. I think I will try transferring the CHARMM36 parameters into a custom OPLS parameter file. Any warnings you can think of off the top of your head? Regards, Steffen
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Hi Steffen, OPLS does not have native support for phosphorylated residues, so there are no bonded parameters and no partial charges. The easiest is to use abs3.2_charmm.prm or abs3.2_charmm36.prm instead (the charge sets between OPLS and CHARMM are generally quite similar). If you want to compare to OPLS runs that have lready been completed, you can also specifically transfer over the parameters from abs3.2_charmm36.prm to merge into a custom copy of abs3.2_opls.prm, but this is a bit more work....
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Hi Andreas, My non-phosphorylated runs have been going great, but I've run into a problem while trying to use phosphoserines. The run aborts with: Warning. Parameter file has no partial charge for biotype 1159 (N ) (encountered for atom # 904 ). This run will terminate unless a suitable charge patch is found.* And so on for every SEP atom in the protein sequence. I'm using the abs3.2_opls.prm parameter file and I see that SEP is defined in there. I'm not why the atoms don't have a partial charge,...
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Hello, I believe that common90.f90 is part of the sources that are provided when obtaining the library from the HSL website: http://www.hsl.rl.ac.uk/catalogue/hsl_ma48.html
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Hi, in your "Makefile.local", simply do not pass "-DLINK_HSL" and it should not try to compile HSL at all (in the docu, this option is included for "FFLAGS"). If that is not enough (it should be, though), you can also set the flag "USE_INTERNAL_HSL" to 0 in "Makefile". I'll ask my colleague about the default location for common90.f90, and we'll get back to you on that. Hope that helps (for now), Andreas
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Alexander Falk posted a comment on discussion Help
Hello All, I am attempting to install Campari but I am running into an error because I do not have the required HSL files. I can locate most of the files on the HSL website but I cannot locate a file called common90.f90, which is listed as required on the Campari download page. Can someone please provide me with a link to this file on the HSL website? Alternatively, I see that the HSL files are optional, but I am not sure how to modify the make file so that they are not required. Can someone please...
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Many thanks! Steffen On Sep 5, 2017, at 10:02 AM, Andreas Vitalis gilthe@users.sf.net<mailto:gilthe@users.sf.net> wrote: Hi Steffen, I just uploaded the code. Best, Andreas Residue phosphorylation in CAMPARI?https://sourceforge.net/p/campari/discussion/961471/thread/a9ee3253/?limit=25#1bf2 Sent from sourceforge.nethttp://sourceforge.net because you indicated interest in https://sourceforge.net/p/campari/discussion/961471/ To unsubscribe from further messages, please visit https://sourceforge.net...
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Hi Steffen, I just uploaded the code. Best, Andreas
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Version 3 released!
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Hi Andreas, That's great! I am looking forward to the late-beta update. Regards, Steffen
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