Activity for Miro
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Miro modified a comment on discussion Help and Feedback
Thanks. I am currently using UCSF Chimera, which is fair enough but slow. The problem with other options is parametrisation. When I'll have the time I might give OpenMM/Smirnoff a go.
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Thanks. I am currently using UCSF Chimera. When I'll have the time I might give OpenMM/Smirnoff a go.
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Is it possible to minimise water and cofactors along with the ligand and the binding site residues? I have tried including them as part of the receptor (both as ATOM and as HETATM, respectively) and verified that they are in input pdbqt, however they are not in the output file. If, on the other hand, I include them as part of the ligand pdbqt file, smina complains about a formatting issue with the input file and refuses to run. Best, Miro
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Confirmed. Compiling with the OB development version solves the issue.
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Yes, it does. So you are using the OpenBabel development version 2.3.90, right?
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Hmm. It is the stable release 2.3.2 installed via the package manager in Ubuntu 14.04......
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No, I compiled it from source (git) last week. I will try the precompiled versio...
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No, I compiled it from source last week. I will try the precompiled version.
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When I run smima on certain pdbqt files: smina --receptor 4w9n_protein.pdbqt --ligand...
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Attached the input files.
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When I run smima in certain pdbqt files: smina --receptor 4w9n_protein.pdbqt --ligand...
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Yes, I am. Removing "-g3" and adding "-O3 -ffast-math -funroll-all-loops -ftree-vectorize...
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Yes, I am. I have removed "-g3" and added "-O3 -ffast-math -funroll-all-loops -ftree-vectorize...
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Using -O3 and -pthread (as opposed to -lpthread) seems to improve the performance...
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Both, but when searching it is more dramatic. What I see already is that Eclipse...
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Both, but when searching is more dramatic. What I see already is that Eclipse by...
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And which libraries would have the highest impact? tcmalloc?
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Hi, it is me again. I have recompiled pharmer on the server and tested it (just dbcreate...
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Thanks, if you want to distribute the binary (6.2 MB) just let me know. It has been...
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OK, the binary I have produced in the virtual machine works out of the box in the...
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OK, the binary I have produced in the virtual machine works out of the box in the...
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OK, the binary I have produced in the virtual machine works out of the box in the...
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I needed to add #include <iostream> to Excluder.cpp, put libsmina in the path and...
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I needed to add #include <iostream> to Excluder.cpp, put libsmina in the path and...
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Ok, it is done. I have built it in a virtual machine running SL5. Let's see if I...
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Ok, I think I am getting a bit closer: g++ -c -o tinyxml/tinystr.o tinyxml/tinystr.cpp...
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I could indeed, were I a programmer, but I am a chemist ;-) One more thing, I have...
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I could indeed, were I a programmer, but I am a chemist ;-)
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Deleted.
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With 1.60, this is the error: In file included from PharmerQuery.cpp:32:0: PharmerQuery.h:50:9:...
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And now this: /home/users/momane/Software/pharmer/boost/include/boost/foreach.hpp:913:96:...
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Thanks. I have tried 1.45, 1.60 and 1.54. None seems to work. I have also tried gcc...
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Thanks. I have tried 1.45, 1.60 and 1.54. None seems to work. I have also tried gcc...
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I am having issues with Boost. Are you still using 1.45?
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Ok, good old Eigen 3.1 seems to solve the issue. Now the problem seem to be Boost...
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Ok, good old Eigen 3.1 seems to solve the issue. Now the problem seem to be Boost...
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Ok, good Eigen 3.1 seems to solve the issue. Now the problem seem to be Boost threads....
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Hello, I am struggling to build pharmer in an old SL5 x64 (RHEL5) sever with gcc...
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Hello, I am struggling to build pharmer in an old SL5 x64 (RHEL5) sever with gcc...
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Yes, adjusting the number and size of the exclusion spheres does the trick. The other...
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Please, find the pharmacophore attached. When I inspect the output sdf there are...
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By the way, is pharmer taking into account the excluded volume?
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OK, I have created a database contaning 605 molecules and some 24,000 conformers....
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Hello, I have just downloaded pharmer with a view to using it as some sort of shape...
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Ok, thank you. So I guess that I need to use pharmer in dbsearch mode, right? What...
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Ok, thank you. So I guess that I need to use pharmer in dbsearch mode, right? What...
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Hello, I have just downloaded pharmer with a view of using it as some sort of shape...
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This is the relevant part of the script (it profits from the fact that the order...
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This is the relevant part of the script (it profits from the fact that the order...
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This is the relevant part of the script (it profits from the fact that the order...
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Thank you for the tip. It is fine. Both 1.41 and 1.60 were compiled from source,...
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OK, it is done. It compiles with gcc 4.8 and Boost 1.60 as long as Boost and Eigen3...
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Hello, We have a server running Scientific Linux 5 and I would like to use smina...
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This is the relevant part of the script (it profits from the fact that the order...
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OK, I have writen a bash script to merge smina's minimised flexible residues back...
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If at least the residue number could be kept, it would be already useful.
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OK, the problem now is that it removes the protein atom types and the residue numbers....
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It works! Thank you. The residue name of the ligand is still modified (which could...
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Thanks a million! I will download the updated code and give it a try ASAP.
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This would be the command line: smina --receptor proteins/${protein}.pdbqt --ligand...
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Hello, I am using smina in order to minimize ligand-protein complexes and I have...
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