trj_cavity Activity
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Activity for trj_cavity
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Tianming Qu posted a comment on discussion General Discussion
Hi, have you solved your problem?
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smit patel posted a comment on discussion General Discussion
Hello all, I'm a new user to gromacs as well as this tool. while installing this package for newer version of gromacs i.e 2022 version, following string of errors happen. Can someone suggest what sort of changes must be made into the makefile so that it can compile properly. the first error i got is not finding the trajectoryanalysis.h file. the source of this file is not found on usr/local/gromacs/lib or include. however while looking for the files into the system i found out that path of this files...
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Mario JU posted a comment on discussion General Discussion
Buenos días tengo problemas para instalar esta herramienta. probé con trj_cavity1.1 y trj_cavity. En este momento estoy usando gromacs 4.6.7 Agradezco cualquier ayuda y estaré atento. adjunto error ++ -c -o trj_cavity.o trj_cavity.cpp g++ src/Atom.cpp src/AtomReader.cpp src/AtomWriter.cpp src/Coordinates.cpp src/Grid.cpp src/ForceField.cpp src/AtomReaderGromacs.cpp -o trj_cavity trj_cavity.o -Wall -w -I/opt/gromacs-4.6/lib/../include/gromacs -g -O1 -B/usr/bin -lm -pthread -ldl -L/opt/gromacs-4.6/lib...
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David Huebert posted a comment on discussion General Discussion
Sorry here is the last attachment:
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Dear Teresa, Thank you very much. I will try again. I got confuse about what I should choose as I thought that the index number was meant to represent what filled the pocket and not what the pocket was made of. I tried this again with as you suggested however, I found I was still having issues with the seed I gave so I just allowed it to be created randomly and it appeared to work. I have here the pse file, pdb and the xvg file. The one thing I want to understand is that there are 5 cavities shown...
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Teresa Paramo posted a comment on discussion General Discussion
Hi again David ;) The index you should use is Protein, because this is the group of atoms you want to find cavities in, right? Apparently the program is not finding cavities between the solvent atoms, and therefore there is just a sphere in the 0,0,0 coordinate because it is initialised there when nothing is found. I think you should use a dimension 6 or 5 instead... also a 1.4 angstrom spacing it is usually fine (approx. radius of a water molecule). Good luck! On Sun, 24 Jan 2021 at 21:20, David...
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Hi David, I feel that this should not be an issue with either gro or xtc files (a different thing would be the tpr file), but I can’t confirm... check that out and let us know! :) Cheers On Sun, 24 Jan 2021 at 19:38, David Huebert davidhuebert@users.sourceforge.net wrote: Dear Teresa, Thank you very much. I read this and a previous post in another discussion to place Gromacs 5.1.4 with Trj_Cavity-2.0.3. My only question is if I submit files .gro and .xtc files from a Gromacs-2020.2 run into the Gromacs5.1.4+Trj_Cavity-2.0.3...
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Dear fellow users, I have been attempting to utilize this program to assess the volume of the catalytic pocket of my small enzyme. The simulation was originally done in gromacs-2020.2, however I also have gromacs-5.1.4 utilizing trj_cavity-2.0.3 (as version 2.1 came up with errors and did not install into gromacs-5.1.4). My protein in question is a small protein of about 180 Amino acids which exists in a water+ion mix. I have read through the paper Efficient Characterization of Protein Cavities within...
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Dear Teresa, Thank you very much. I read this and a previous post in another discussion to place Gromacs 5.1.4 with Trj_Cavity-2.0.3. My only question is if I submit files .gro and .xtc files from a Gromacs-2020.2 run into the Gromacs5.1.4+Trj_Cavity-2.0.3 will there be issues with reading the files? -David
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Hi David, As stated in the home page: trj_cavity v2 runs in parallel and supports GROMACS v5.1+ series. If you want to continue on using GROMACS v4.x, please use trj_cavity_v1.1. As I have recollected from other discussions, versions after the 5.x series changed the API once again so previous third party applications such as trj_cavity v2 are not compatible (v2 was already refactored from v1 to be compatible with those versions). In summary, v1 goes with gromacs4 and v2 with gromacs 5.1+. Hope this...
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Hello, I have been attempting to install version 2.1 which in the file is labelled 2.0 after tar. I am utilizing Ubuntu 20.04 if that makes a difference. I have attempted to install this on both Gromacs 2020.2 as well as Gromacs-4.6.7. Should I use a specific version for this program as I wish to enter xtc files into it and not turn that into PDB files. The error is the same no matter these 2 versions: $ make g++ src/Atom.cpp src/Mapper.cpp src/Writer.cpp src/Coordinates.cpp src/Grid.cpp src/ForceField.cpp...
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Christie Sandall posted a comment on discussion General Discussion
Hi there, Having issues with installation and hoping for some assistance. The first time I ran "make", I received the following error: ~/bin/trj_cavity_v2.0$ make c++ -c -o trj_cavity.o trj_cavity.cpp g++ src/Atom.cpp src/Mapper.cpp src/Writer.cpp src/Coordinates.cpp src/Grid.cpp src/ForceField.cpp src/Reader.cpp src/CavityOptions.cpp src/FilePointers.cpp src/CavityParams.cpp src/InputUtils.cpp src/ReaderGromacs.cpp src/MapperGromacs.cpp -o trj_cavity trj_cavity.o -Wl,-rpath=/usr/local/gromacs/lib...
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Shamim Shadfar posted a comment on discussion General Discussion
Hello, I am trying to install try_cavity (with gromacs - version 5). However, make fails with the error: ld: unknown option: -rpath=/usr/local/gromacs/lib collect2: error: ld returned 1 exit status If we remove -Wl,-rpath=$(GMXLDLIB) from the LDFLAGS, or if we turn the "=" into a "," so it is passed to LD as separate arguments, make fails with: ld: symbol(s) not found for architecture x8664. At this point I don't know where to go next. It might be an accidental mixture of 32 bit and 64 bit libraries....
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Farzane modified a comment on discussion General Discussion
Dear Teresa, First, thank you so much for the creation of this tool. I am having the following error when I compile trj_cavity. Would you please guide me? g++ src/Atom.cpp src/Mapper.cpp src/Writer.cpp src/Coordinates.cpp src/Grid.cpp src/ForceField.cpp src/Reader.cpp src/CavityOptions.cpp src/FilePointers.cpp src/CavityParams.cpp src/InputUtils.cpp src/ReaderGromacs.cpp src/MapperGromacs.cpp -o trj_cavity trj_cavity.o -Wl,-rpath=/usr/local/gromacs/lib -I/usr/local/gromacs/lib/../../include -L/usr/local/gromacs/lib...
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Dear Teresa, First, thank you so much for the creation of this tool. I am having the following error when I compile trj_cavity. Would you please guide me? g++ src/Atom.cpp src/Mapper.cpp src/Writer.cpp src/Coordinates.cpp src/Grid.cpp src/ForceField.cpp src/Reader.cpp src/CavityOptions.cpp src/FilePointers.cpp src/CavityParams.cpp src/InputUtils.cpp src/ReaderGromacs.cpp src/MapperGromacs.cpp -o trj_cavity trj_cavity.o -Wl,-rpath=/usr/local/gromacs/lib -I/usr/local/gromacs/lib/../../include -L/usr/local/gromacs/lib...
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Zaved Hazarika posted a comment on discussion General Discussion
Hello Folks I am trying to install trj_cavity but getting an error: fatal error: gromacs/trajectoryanalysis.h: No such file or directory #include "gromacs/trajectoryanalysis.h" However I have edited the Makefile and updated the CFLAGS as necessary: CFLAGS = -Wall -w -O1 -I/soft/gmx514/include/gromacs I am still getting the same error. Kindly help. Thank You Regards Zaved
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Urooj Qureshi posted a comment on discussion General Discussion
Hello! i am a new user of trj_cavity with no gromacs, i used following command to calculate volume of the pocket ./trj_cavity_ng -s ../md_0_1.tpr -f ../md_0_1.xtc -n index-activesite.ndx -ov volume.xvg -o cavity.pdb but i got empty files with error : �@B file does not exist! what can i do?
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Anna Troya posted a comment on discussion General Discussion
Okay yeah it is taking the system coordinate, thus following the numbering of the seed I provide. I can find out with VMD! Thanks for the time anyway!! Best, Anna
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Thanks for the reply! :) In relation to my first post (same commands and same output), I have a second question: In the output file I provided, the x-axis is the position along the pore in A. How can I link that to my protein? or How does the program set the position?Because I am providing a seed in the command so I would expect that to be the 0, and then z-axis upwards positive and z-ax downwards negative distance in A. But my pore goes from 53 to 90A, where my seed is included. Is the program taking...
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manikya posted a comment on a wiki page
Hello, I am trying to install trj_cavity v2.0 with version of Gromacs (version 5.1.2). Unfortunately, following error has happened. bioinfo2@bioinfo2-Vostro-3470:~/manikya/tunnel_volume/trj_cavity_v2.0$ make Makefile:25: *** "GMXLDLIB not found, please source GMXRC. If you want to build the stand-alone version, type: make no_gromacs". Stop.
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Hello, I am trying to install trj_cavity v2.0 with version of Gromacs (version 5.1.2). Unfortunately, following error has happened. bioinfo2@bioinfo2-Vostro-3470:~/manikya/tunnel_volume/trj_cavity_v2.0$ make Makefile:25: *** "GMXLDLIB not found, please source GMXRC. If you want to build the stand-alone version, type: make no_gromacs". Stop.
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Hello Anna, It is the standard deviation. All the best
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Dear users, I have used the following command to run trj_cavity on my protein of interest to find a cavity: trj_cavity -s prot.pdb -f prot-traj.xtc -dim 5 -spacing 1.4 -seed 79.6 81.4 83.5 -cutoff 10 -o cavity.pdb -ov volume.xvg -ob tunnel.pdb -obt tunnel_traj.xtc -obs sector_profile.xvg -oba bottleneck.xvg -n index_restricted.ndx On the output file sector_profile.xvg I get the following: @ xaxis label "Axis value (Angstroms)" @ yaxis label "Area (Angstroms\S2\N)" 53 4.590 2.419 54 29.049 33.503...
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alison popp posted a comment on discussion General Discussion
Hi, I am really liking this software, owever, there seems to be a problem with the -obt option. the program start then "Segmetation fault (core dumped)" message shows and the calculations are dropped. -ob, -o and -ot all run smoothly though. Would you mind taking a look? apop29
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Uff, I am glad! Have fun :)
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Yoav posted a comment on discussion General Discussion
Hi Teresa, I got it to work with gromacs 5.1.4 and with version 2.0.3 of trj_cavity. Everything seems to be working great. Thanks a lot for all of your assistance and for developing this awesome tool!
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well i tried compiling trj cavity with gcc (as i did with gromacs) and i'm getting the same error so I really just don't know. I'll try to repeat it on another machine and see how it goes there.
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I would not work - according to the license of gromacs, the library needs to be remain external because they forbid its distribution, and you are having problems with gromacs. In this thread, somebody had the same issue as you with gromacs 5.1.4, and made it work... https://sourceforge.net/p/trjcavity/discussion/general/thread/312ce4ae/ So the sources are ok, the problem lays in your system. Some other users had problems because they were mixing compilers - that is, they compiled gromacs and trj_cavity...
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come to think of it, any chance you have a compiled binary that you could email me ?
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I've used a solution that you previously suggested for someone with a similar error and this is what I'm getting now ++ /mnt/c/Users/yoavar/trj_cavity_v2.0/src/Atom.cpp /mnt/c/Users/yoavar/trj_cavity_v2.0/src/Mapper.cpp /mnt/c/Users/yoavar/trj_cavity_v2.0/src/Writer.cpp /mnt/c/Users/yoavar/trj_cavity_v2.0/src/Coordinates.cpp /mnt/c/Users/yoavar/trj_cavity_v2.0/src/Grid.cpp /mnt/c/Users/yoavar/trj_cavity_v2.0/src/ForceField.cpp /mnt/c/Users/yoavar/trj_cavity_v2.0/src/Reader.cpp /mnt/c/Users/yoavar/trj_cavity_v2.0/src/CavityOptions.cpp...
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Sorry, I meant newer - one with that problem solved.
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Well, so we have reached an impass here. trj_cavity works under the gnu compiler collection but boost is c11 and it seems that they won´t co-exist. If you manage to run without declaring that libary on the makefile, cool. Otherwise go for an older gromacs version, because it seems that this one does not have their analysis suite well configured.
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GROMACS does indeed work on my pc.
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Yes GROMACS does work on my pc.
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Yes it does work on my pc.
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You must have upset the Makefile somewhere, because "numberOfColumns" does exist in src/ForceField.cpp... Does that gromacs even work on your PC? Because that boost libary is for gromacs not for trj_cavity, and you dont really need to declare it here (and apparently something on that libary is upsetting trj_cavity, thats why is not declared in the first place). As a rule of thumb, if gromacs does not work in you computer, it wont work with trj_cavity either, so please make sure it is correctly i...
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I actually did install boost and added this line to the LDFLAGS in the makefile LDFLAGS = -Wl,-rpath=$(GMXLDLIB) -I$(GMXLDLIB)/../include -L$(GMXLDLIB) -lgromacs -L/usr/lib -I/usr/include -I$(GMXLDLIB)/../include/gromacs/external/boost/ and now i'm getting this error instead: g++ src/Atom.cpp src/Mapper.cpp src/Writer.cpp src/Coordinates.cpp src/Grid.cpp src/ForceField.cpp src/Reader.cpp src/CavityOptions.cpp src/FilePointers.cpp src/CavityParams.cpp src/InputUtils.cpp src/ReaderGromacs.cpp src/MapperGromacs.cpp...
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Check out, the error is: gromacs/analysisdata/abstractdata.h:46:32: fatal error: boost/shared_ptr.hpp: No such file or directory It looks like gromacs require the boost libary installed. Check their installation page, they are usually quite comprehensive.
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this is what i got with GMX 5.1.4 and trjcav2 g++ src/Atom.cpp src/Mapper.cpp src/Writer.cpp src/Coordinates.cpp src/Grid.cpp src/ForceField.cpp src/Reader.cpp src/CavityOptions.cpp src/FilePointers.cpp src/CavityParams.cpp src/InputUtils.cpp src/ReaderGromacs.cpp src/MapperGromacs.cpp -o trj_cavity trj_cavity.o -Wl,-rpath=/usr/local/gromacs/lib -I/usr/local/gromacs/lib/../include -L/usr/local/gromacs/lib -lgromacs -L/usr/lib -I/usr/include -lm -lpthread -ldl -fopenmp -Wall -w -O1 src/Grid.cpp:113:13:...
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i'm currently installing gromacs 5.1.4 which I noticed that in a previous post, was found to work correctly with trj cavity 2. Once I'll finish getting it compiled i'll give trj cavity 2 another try and if that fails i'll give another go to GMX 4.6.7 and trj cavity 1.1. Thanks for your help in this it is much appreciated!
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When gromacs gets installed, it stores in your system a variable called GMXLIB/GMXLDLIB (depending on the version of gromacs) containing the path of the gromacs libraries - I use that variable to find them too. You can check its value with: echo $GMXLDLIB if that does not exist, you can initialize it by running source "wherever_your_gromacs_program_is_installed"/bin/GMXRC A last thing, if you are choosing a version of gromacs, if you use the 5.x series (or even the 2016 series, I think it also works...
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About the version 1.1 with Gormacs 4.6.7 it should work fine (I have been using myself that combination in the past without any problem). Can you post me the input line and the full trace of that segmentation fault? Cheers
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fair enough...then could you just give me a quick explenation of the LDflags operators and which libraries are called by which one of them ?
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About the version 2018, it seems Gromacs has again changed the API of their analysis libary (I don´t think they regard other apps using their libraries at all). Hence once again I would need to create a new version of the trj_cavity program to add these modifications because they would be incompatible with older versions of Gromacs - I guess there is a point one should surrender, and probably this is... But you can add the modifications yourself to the code, it is open source after all :)
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EDIT: I did successfully install the 1.1 version of the program but I keep getting segmentation faults with it no matter what I do so I'm trying to compile the v2.1 now instead with no sucesss so far :( (the error above happened with the 2.1 version of the code)
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EDIT: I did successfully install the 1.1 version of the program but I keep getting segmentation faults with it no matter what I do so I'm trying to compile the v2.1 now instead with no sucesss so far :(
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Hi again, actually this has become irrelevant, i succeeded in compiling it correctly now :) all the best !
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Dear Teresa, Thank you for making this program, it seems exceptionally useful but unfortunatley i'm having a issues with compiling it. The error i'm getting is this: src/MapperGromacs.cpp: In member function ‘Atom MapperGromacs::readTrjAtom(const t_trxframe&, t_topology, int)’: src/MapperGromacs.cpp:51:5: error: ‘radii’ was not declared in this scope if(radii!=NULL){ ^ src/MapperGromacs.cpp:52:22: error: ‘it’ was not declared in this scope int index_radii = it - offset; ^ src/MapperGromacs.cpp:52:27:...
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Yin Chang modified a comment on discussion General Discussion
Hi, I ran a system with three polymer chains surrounding a box of water molecules and one glucose monomer. After running equilibrium, I want to use trjcavity to find out all possible cavities (>1 anstrom) between polymer/water, water/water, or water/glucose. I have questions about to choose the proper settings of both grid spacing, and dimension. I tried -spacing 1 first and expect to find out more cavities than -spacing 1.4. However, the results are inverse as attached figure 1 (-spacing 1, -dim...
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Hi, I ran a system with three polymer chains surrounding a box of water molecules and one glucose monomer. After running equilibrium, I want to use trjcavity to find out all possible cavities (>1 anstrom) between polymer/water, water/water, or water/glucose. I have questions about to choose the proper settings of both grid spacing, and dimension. I tried -spacing 1 first and expect to find out more cavities than -spacing 1.4. However, the results are inverse as attached figure 1 (-spacing 1, -dim...
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Problem solved. I just solved it by copying both trj_cavity and AtomRadii.txt to my running files, then this problem solved. I guess maybe somewhere wrong when I compile trj_cavity with gromacs. Thanks. Yin
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Hi, I am using trj_cavity (v2.1) gromacs version (5.1.1) to calculate free volume change in the trajectory(.xtc). I have one polymer chain, and water in my system. Here is my command: trj_cavity -s NeuGlu.pdb -f frame100ps.xtc -o cavity.pdb -ostat stat.pdb Only C, H, O in my pdb file. I get every output empty. While running, I keep getting the same error message "File AtomRadii.txt not found! Using default values file does not exist!" I have check the AtomRadii.txt file in the trj_cavity program...
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Marcelo Depolo Poleto posted a comment on discussion General Discussion
Hi, I've downloaded the last version (2.1) of trj_cavity. I've both GROMACS 5.0.7 and 5.1.4 installed in my machine using '/usr/local/gromacs_507/' and '/usr/local/gromacs_514/' as directories for their installation. Still, when I try to run 'sudo make' inside trj_cavity, I get an error: "Makefile:25: *** "GMXLDLIB not found, please source GMXRC. If you want to build the stand-alone version, type: make no_gromacs" " And if I try to manually source the GMXRC (by typping "source /usr/local/gromacs_514/bin/GMXRC"...
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Rajeswari posted a comment on discussion General Discussion
Hi, I am trying to install trajcavity with gromcas 5.1.4. During installation, i get the following error. Please suggest me how should I rectify this? /usr/local/gromacs5.1.4/lib/libgromacs.a(fft_fftw3.cpp.o): In function gmx_fft_destroy': fft_fftw3.cpp:(.text+0x22c3): undefined reference tofftwf_destroy_plan' fft_fftw3.cpp:(.text+0x2317): undefined reference to fftwf_free' /usr/local/gromacs5.1.4/lib/libgromacs.a(fft_fftw3.cpp.o): In functiongmx_fft_get_version_info': fft_fftw3.cpp:(.text+0x25c1):...
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Nemanja Djokovic posted a comment on discussion General Discussion
Dear Teresa, That worked just great. Thank you! I have already tried trj_cavity, and it's briliant. Kind regards, Nemanja
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Hi Nemanja, It is a bit weird the boost libary of gromacs is there... Maybe you could try to add boost to the libary path by adding it in the Makefile: LDFLAGS = -Wl,-rpath=$(GMXLDLIB) -I$(GMXLDLIB)/../include -L$(GMXLDLIB) -lgromacs -L/usr/lib -I/usr/include -I$(GMXLDLIB)/../include/gromacs/external/boost/ Let me know if this works...
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Hi Teresa, I am using 5.1.4 version. Thank you for response.
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Hi Teresa, I am using 5.1.4 version. Thank you for responce.
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Hi Nemanja, It looks like the error comes from gromacs... which version do you use? Cheers
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Dear all, First problem I faced have already been described here (fatal error: gromacs/trajectoryanalysis.h), so Ive solved it successfully by making sugested changes in make file (LDFLAGS = -Wl,-rpath=$(GMXLDLIB) -I$(GMXLDLIB)/../include -L$(GMXLDLIB) -lgromacs -L/usr/lib -I/usr/include). After this, I faced another error: "~~~ g++ src/Atom.cpp src/Mapper.cpp src/Writer.cpp src/Coordinates.cpp src/Grid.cpp src/ForceField.cpp src/Reader.cpp src/CavityOptions.cpp src/FilePointers.cpp src/CavityParams.cpp...
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Hi Balaji, Have you checked if the file (for example) /usr/local/gromacs/lib64/../include/gromacs/analysisdata/analysisdata.h exists? Cheers
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Balaji posted a comment on discussion General Discussion
Hi Teresa, I am trying to install trj_cavity with gromacs 5.1.4. Before writing this mail, I have edited Makefile by looking to the old post and tried to install but i couldn't succeeded. I got the error as g++ src/Atom.cpp src/Mapper.cpp src/Writer.cpp src/Coordinates.cpp src/Grid.cpp src/ForceField.cpp src/Reader.cpp src/CavityOptions.cpp src/FilePointers.cpp src/CavityParams.cpp src/InputUtils.cpp src/ReaderGromacs.cpp src/MapperGromacs.cpp -o trj_cavity trj_cavity.o -Wl,-rpath=/usr/local/gromacs/lib64...
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Willy Evangelista posted a comment on discussion General Discussion
You were right, the parameters were different. I followed your suggestions and everything worked just great!! Thank you so much for all your help. Cheers. W.
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Hi Willy, The cavity.pdb file is the cavity correspoding to the first frame of the trajectory, so if you get a different result it means that either the first frame is different in the two trajectories or the parameters used when running the program are different each time - otherwise you should get the same result... By the way, if you generate the trajectory (-ot) you can see the trajectory of the cavities; with the cambination of parameters "-seed" and "-max" you can restrict the output to the...
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Hey Teresa: Good news: I moved everything to another machine with 10-times more memory and worked very well with the full trajectory. "Bad news": using the same topology file and the same trajectory, but specifying different end points A) 0-100ns and B) 0-1000ns, I obtained different cavity.pdb files. The cavity that I am interested in is present in the first case (A), but this cavity is missing in the second case (B). So, I was wondering: What frame is this cavity.pdb file based on? Since I am interested...
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No problem at all! Anyway, if you think there might be a problem with some specific frame, let me know so I can do some tests on it! :)
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I tried with the "-np 1" option, but still getting the same error. However, I can analyzed up to 120ns, this should be enough because I can split my trajectories to make it work. Thanks so much for your help!!! Cheers W.
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Cool! I am glad it works now :) There can be some problems in trj_cavity with very large trajectories when running in parallel, as you could potentially use up all your memory... However, the error would not be a segmentation fault (I think). Can you try to run the long trajectory with one single processor (i.e. using option "-np 1")? With this option I don't keep the trajectory in memory, so then we can see if the problem is about memory or there is another bug... Thanks!
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Well, I recompiled gromacs and got a different error message, something related to trajectoryanalysis.h not found. So, I used the solution you suggested in another post and... it worked!!! It works good for short trajectories. Is there any limit in the number of frames in the trajectory? I ask this because I got a "Segmentation fault (core dumped)" error when I tried a trajectory of 1000 ns. Thank you so much for you assistance. W.
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Hey Teresa: Yeah, it is weird. I could create the non-gromacs version, it seems to work fine. I tested it just with one frame in pdb format and checked out in pymol, looks good. I think I compiled gromacs before updating Ubuntu, I will double check that. But, right, now my g++ compiler is: ~$ g++ --version g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 20160609 Copyright (C) 2015 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even...
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Hi Willy, The trj_cavity.cpp file being empty is OK, I just use it to create the target executable. It is bit weird, because everything in your system looks ok... Maybe is some incompatibility with the compiler (you compiled gromacs with a different compiler?). Can you create the non-gromacs version? Cheers
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Thanks for your prompt reply. let's see, these are the contents of the folders: $ ls /usr/local/gromacs/lib/x86_64-linux-gnu/ libgromacs.so libgromacs.so.1 libgromacs.so.1.1.0 pkgconfig $ ls /usr/local/gromacs/lib/x86_64-linux-gnu/../../include/ gromacs and $ echo $LD_LIBRARY_PATH /usr/local/gromacs/lib/x86_64-linux-gnu $ echo $GMXLDLIB /usr/local/gromacs/lib/x86_64-linux-gnu About the trj_cavity.cpp with zero bytes, is this alright? Thanks W.
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Hi Willy, It looks like trj_cavity can't find the gromacs library headers... Can you tell me if the folder /usr/local/gromacs/lib/x86_64-linux-gnu -I/usr/local/gromacs/lib/x86_64-linux-gnu/../../include exists? If not, the path will have to be changed in the Makefile... Cheers, Teresa
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I forgot to mention, it is gromacs 5.1.1
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Hi Teresa: I getting this error when I try to compile trj_cavity, latest version accordin with the website, something that I notices is that trj_cavity.cpp has zero bytes, wherease trj_cavity_ng.cpp has 256 bytes. Can you help me with this, please? ~/Downloads/cavity/trj_cavity_v2.0$ make g++ src/Atom.cpp src/Mapper.cpp src/Writer.cpp src/Coordinates.cpp src/Grid.cpp src/ForceField.cpp src/Reader.cpp src/CavityOptions.cpp src/FilePointers.cpp src/CavityParams.cpp src/InputUtils.cpp src/ReaderGromacs.cpp...
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Hi Tap, Thankas for trying trj_vcavity, and for providing feedback! Unfortunately,...
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Tap Ha-Duong posted a comment on discussion General Discussion
Dear Teresa, I also would like to thank you for the development of trj_cavity that...
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Hi Gustavo, What do you have in your GMXLDLIB? Just to understand which gromacs version...
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Gustavo Avelar Molina modified a comment on discussion General Discussion
Dear all, I've just installed GROMACS 5.1.2 on Linux and tried to install trj_cavity....
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Dear all, I've just installed GROMACS 5.1.2 and tried to install trj_cavity. However,...
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Dear all, I tried to install trj_cavity 2.1 with GROMACS 2016.1 on Linux, but I was...
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rahmad akbar posted a comment on discussion General Discussion
I'll give it a try. As always thank you for your help and happy holidays.
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I think the problem is that the protein in the first frame (the tpr file) is in a...
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Hi Tere, Super thanks!! I succesfully compiled and ran the program. However, the...
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Hi Rahmad, I think this error might be easy to solve, just do to the Makefile and...
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Hi Tere, Thanks for the quick reply, I attempted to instal on a linux but I ran into...
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Hi Rahmnad, Currently I am only supporting Linux distributions, but your error indicates...
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Hello there, I encountered the following error when attempting to install on OSX...
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Hi Maximilien, The version 2.0 had some bugs regarding to the calcultion of tunnels....
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Maximilien posted a comment on discussion General Discussion
Thank you for your answer ! This the version 2.0 compiled with C++ Intel icpc version...
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Hi Maximilien, I inderstand you did not install the program yourself, but can you...
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Hello, I have a problem with my analyzes and I hope you will be able to help me....
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Anu Chandra posted a comment on discussion General Discussion
Hi Paramo, Thanks for the reply. I think the version I installed is the latest one....
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Hi Anu, Please, try to use the latest version, i.e. 2.1 instead of 2.0.x because...
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Hello Paramo, Adding to my previous comment, trj_cavity runs sucessfully when I provide...
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Hi, Thanks for your reply. As you mentioned, I have downgraded the gromcas version...
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Hi Anu, It seems that once again this version of gromacs has changed the API of the...
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Hello, In order to overcome the issue mentioned above, I tried to install trj_cavity...
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Hello, I am trying to install trj_cavity v2.0 with latest version of Gromacs (version...
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HI Stephen, I think the problem is that you are providing just one group when asked...
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