[gmx-users] how to make whole trajectory Pdb files
Hello Everyone, Pls tell me after doing simulation, which command should i use ,so that i can get all the pdb files of whole trajectory. I know the command where i can get one pdb file at a time, i.e. trjconv -f *_vac_md_1ns.xtc -s *_vac_md_1ns.tpr -dt 20 -b 0 -e 300 -o _vac_md_1ns_300.pdb trjconv -f *_vac_md_1ns.xtc -s *_vac_md_1ns.tpr -o *_vac_md_1ns_dump_300.pdb -dump 300 This command will give me pdb file for 300ps file where my total simulation is for 1 ns. but how to get whole pdb files for the simulation of 1ns where my dt=0.2 This is a very silly problem. But Please help me out. With Regards Bhawana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to make whole trajectory Pdb files
Bhawana Gupta wrote: Hello Everyone, Pls tell me after doing simulation, which command should i use ,so that i can get all the pdb files of whole trajectory. I know the command where i can get one pdb file at a time, i.e. trjconv -f *_vac_md_1ns.xtc -s *_vac_md_1ns.tpr -dt 20 -b 0 -e 300 -o _vac_md_1ns_300.pdb trjconv -f *_vac_md_1ns.xtc -s *_vac_md_1ns.tpr -o *_vac_md_1ns_dump_300.pdb -dump 300 This command will give me pdb file for 300ps file where my total simulation is for 1 ns. but how to get whole pdb files for the simulation of 1ns where my dt=0.2 This is a very silly problem. But Please help me out. -sep With Regards Bhawana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to avoid the error: Shake block crossing node boundaries
I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation 'pbc=no' which makes to use particle decomposition option -pd of mdrun. In this case the automatic particle distribution over the nodes leads to the error: Fatal error: Shake block crossing node boundaries constraint between atoms (11191,11193) In the previous version 3.3 I used manual balancing with the -load option to avoid the problem. In the current version 4.0 I did not find anything similar for the particle decomposition. Is there a way to run parallel simulations of the protein in vacuum? Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to avoid the error: Shake block crossing node boundaries
Leontyev Igor wrote: I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation 'pbc=no' which makes to use particle decomposition option -pd of mdrun. In this case the automatic particle distribution over the nodes leads to the error: Fatal error: Shake block crossing node boundaries constraint between atoms (11191,11193) In the previous version 3.3 I used manual balancing with the -load option to avoid the problem. In the current version 4.0 I did not find anything similar for the particle decomposition. Is there a way to run parallel simulations of the protein in vacuum? I'd suggest updating to 4.0.4 for the copious bug fixes, one of which might solve your problem. I can't think of a good reason offhand why PD or DD should be necessary for non-PBC simulations in vacuo - try both. If you've still got your problem, let us know. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem in simulation of DMPC lipid bilayer
Dear all, I am using DMPC lipid bilayer from teleman sir website to insert my protein in this lipid bilayer .I have done this by using command genbox. After that when I have run the command - pdb2gmx -f tap-in-dmpc.pdb -o tap-in-dmpc.gro -p tap-in-dmpc.top -i tap-in-dmpc-itp -ff oplsaa Error like this- There are 0 hydrogen bonds Warning: 'DMP' not found in residue topology database, trying to use 'DMSO' --- Program pdb2gmx, VERSION 4.0.3 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom C1 in residue DMSO 1 not found in rtp entry with 10 atoms while sorting atoms --- so please tell me how can I add DMP in residue topology database if anyone has knowledge about this. And please if also u know about any site of lipid bilayer from where i can download lipid bilayer then let me know. thanks in advance Nitu Sharma School of life siences Jawaherlal Nehru University New Delhi ,India --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] k- means clustering
Hi everyone, I want to know whether anyone has done k-means clustering using gromacs 3.3.1. I saw that one program has been contributed to do k-means clustering using g_cluster. Has anyone tried to use this program to do such clustering. I would also like to know the correct command option to cluster conformations based on pairwise rmsd using g_cluster. Any suggestion will be extermely helpful. Thanks in advance Sarbani___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] k- means clustering
sarbani chattopadhyay wrote: Hi everyone, I want to know whether anyone has done k-means clustering using gromacs 3.3.1. I saw that one program has been contributed to do k-means clustering using g_cluster. Has anyone tried to use this program to do such clustering. I don't know. Providing a link would be a good start for people to know what you are talking about. I would also like to know the correct command option to cluster conformations based on pairwise rmsd using g_cluster. g_cluster -h Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in simulation of DMPC lipid bilayer
nitu sharma wrote: Dear all, I am using DMPC lipid bilayer from teleman sir website to insert my protein in this lipid bilayer .I have done this by using command genbox. After that when I have run the command - pdb2gmx -f tap-in-dmpc.pdb -o tap-in-dmpc.gro -p tap-in-dmpc.top -i tap-in-dmpc-itp -ff oplsaa Error like this- There are 0 hydrogen bonds Warning: 'DMP' not found in residue topology database, trying to use 'DMSO' --- Program pdb2gmx, VERSION 4.0.3 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom C1 in residue DMSO 1 not found in rtp entry with 10 atoms while sorting atoms --- so please tell me how can I add DMP in residue topology database if anyone has knowledge about this. And please if also u know about any site of lipid bilayer from where i can download lipid bilayer then let me know. You may find some helpful information http://wiki.gromacs.org/index.php/Membrane_Simulations and http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re:Re: [gmx-users] How to avoid the error: Shake block crossing nodeboundaries
Leontyev Igor wrote: I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation 'pbc=no' which makes to use particle decomposition option -pd of mdrun. In this case the automatic particle distribution over the nodes leads to the error: Fatal error: Shake block crossing node boundaries constraint between atoms (11191,11193) In the previous version 3.3 I used manual balancing with the -load option to avoid the problem. In the current version 4.0 I did not find anything similar for the particle decomposition. Is there a way to run parallel simulations of the protein in vacuum? I'd suggest updating to 4.0.4 for the copious bug fixes, one of which might solve your problem. I can't think of a good reason offhand why PD or DD should be necessary for non-PBC simulations in vacuo - try both. If you've still got your problem, let us know. Mark Gromacs-4.0.4, which I use, does not allow DD in non-PBC simulations. Only PD options is available. But PD has no flexibility to manually redistribute particles over the nodes. As written in the manual With PD only whole molecules can be assigned to a processor. Does it mean that there is no way to start PD parallel simulations of whole protein? In other words, does it means that there is no way to run parallel simulation of protein in vacuum? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to avoid the error: Shake block crossing nodeboundaries
Igor Leontyev wrote: Leontyev Igor wrote: I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation 'pbc=no' which makes to use particle decomposition option -pd of mdrun. In this case the automatic particle distribution over the nodes leads to the error: Fatal error: Shake block crossing node boundaries constraint between atoms (11191,11193) In the previous version 3.3 I used manual balancing with the -load option to avoid the problem. In the current version 4.0 I did not find anything similar for the particle decomposition. Is there a way to run parallel simulations of the protein in vacuum? I'd suggest updating to 4.0.4 for the copious bug fixes, one of which might solve your problem. I can't think of a good reason offhand why PD or DD should be necessary for non-PBC simulations in vacuo - try both. If you've still got your problem, let us know. Mark Gromacs-4.0.4, which I use, does not allow DD in non-PBC simulations. Only PD options is available. But PD has no flexibility to manually redistribute particles over the nodes. As written in the manual With PD only whole molecules can be assigned to a processor. Does it mean that there is no way to start PD parallel simulations of whole protein? In other words, does it means that there is no way to run parallel simulation of protein in vacuum? You can do it the way all the other programs do: only use constraints on bonds involving H, and reducing the timestep to 1 fs. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to make pdb file of whole trajectory
Hello everyone, Thankyou for the reply for my previous message. But sorry to say I didn't get, what you want to say. Please tell me in elaborated way. I will be thankful. With Regards Bhawana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to make pdb file of whole trajectory
Bhawana Gupta wrote: Hello everyone, Thankyou for the reply for my previous message. But sorry to say I didn't get, what you want to say. Please tell me in elaborated way. I will be thankful. trjconv -sep With Regards Bhawana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to avoid the error: Shake blockcrossing nodeboundaries
Leontyev Igor wrote: I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation 'pbc=no' which makes to use particle decomposition option -pd of mdrun. In this case the automatic particle distribution over the nodes leads to the error: Fatal error: Shake block crossing node boundaries constraint between atoms (11191,11193) In the previous version 3.3 I used manual balancing with the -load option to avoid the problem. In the current version 4.0 I did not find anything similar for the particle decomposition. Is there a way to run parallel simulations of the protein in vacuum? I'd suggest updating to 4.0.4 for the copious bug fixes, one of which might solve your problem. I can't think of a good reason offhand why PD or DD should be necessary for non-PBC simulations in vacuo - try both. If you've still got your problem, let us know. Mark Gromacs-4.0.4, which I use, does not allow DD in non-PBC simulations. Only PD options is available. But PD has no flexibility to manually redistribute particles over the nodes. As written in the manual With PD only whole molecules can be assigned to a processor. Does it mean that there is no way to start PD parallel simulations of whole protein? In other words, does it means that there is no way to run parallel simulation of protein in vacuum? You can do it the way all the other programs do: only use constraints on bonds involving H, and reducing the timestep to 1 fs. I try to run MD with only constrained h-bonds (constraints = hbonds) which allow 2fs timestep. The timestep 1fs would be needed if there will be vibrating (unconstrained) h-bonds. But you suggest to use constraints or it was a misprint? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] k means cluster
Hi, Actually I was referring to the following post where the attempt to incorporate the method of k means clustering in gromacs has been discussed. http://www.mail-archive.com/gmx-users@gromacs.org/msg05089.html Has anyone tried to use this ? Thanks in advance Sarbani ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to avoid the error: Shake blockcrossing nodeboundaries
Igor Leontyev wrote: Leontyev Igor wrote: I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation 'pbc=no' which makes to use particle decomposition option -pd of mdrun. In this case the automatic particle distribution over the nodes leads to the error: Fatal error: Shake block crossing node boundaries constraint between atoms (11191,11193) In the previous version 3.3 I used manual balancing with the -load option to avoid the problem. In the current version 4.0 I did not find anything similar for the particle decomposition. Is there a way to run parallel simulations of the protein in vacuum? I'd suggest updating to 4.0.4 for the copious bug fixes, one of which might solve your problem. I can't think of a good reason offhand why PD or DD should be necessary for non-PBC simulations in vacuo - try both. If you've still got your problem, let us know. Mark Gromacs-4.0.4, which I use, does not allow DD in non-PBC simulations. Only PD options is available. But PD has no flexibility to manually redistribute particles over the nodes. As written in the manual With PD only whole molecules can be assigned to a processor. Does it mean that there is no way to start PD parallel simulations of whole protein? In other words, does it means that there is no way to run parallel simulation of protein in vacuum? You can do it the way all the other programs do: only use constraints on bonds involving H, and reducing the timestep to 1 fs. I try to run MD with only constrained h-bonds (constraints = hbonds) which allow 2fs timestep. The timestep 1fs would be needed if there will be vibrating (unconstrained) h-bonds. But you suggest to use constraints or it was a misprint? This is subject to discussion, see e.g. gromacs manual. Actually, with all bonds constrained 2 fs is already a large time step, and with only bonds containing H constrained 1 fs is also quite large. A further discussion can be found in the P-Lincs paper IIRC (J. Chem. Theor. Comp. 4 (2008) p. 116). ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to make pdb file of whole trajectory
Bhawana Gupta wrote: Hello everyone, Thankyou for the reply for my previous message. But sorry to say I didn't get, what you want to say. Please tell me in elaborated way. I will be thankful. Your example commands look like you already have a trajectory file with the whole trajectory. Use trjconv if you just want to convert from one format to another. David thinks you are asking how to get a separate PDB file for each frame. If not, please explain further. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to avoid the error:Shake blockcrossing nodeboundaries
Leontyev Igor wrote: I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation 'pbc=no' which makes to use particle decomposition option -pd of mdrun. In this case the automatic particle distribution over the nodes leads to the error: Fatal error: Shake block crossing node boundaries constraint between atoms (11191,11193) In the previous version 3.3 I used manual balancing with the -load option to avoid the problem. In the current version 4.0 I did not find anything similar for the particle decomposition. Is there a way to run parallel simulations of the protein in vacuum? I'd suggest updating to 4.0.4 for the copious bug fixes, one of which might solve your problem. I can't think of a good reason offhand why PD or DD should be necessary for non-PBC simulations in vacuo - try both. If you've still got your problem, let us know. Mark Gromacs-4.0.4, which I use, does not allow DD in non-PBC simulations. Only PD options is available. But PD has no flexibility to manually redistribute particles over the nodes. As written in the manual With PD only whole molecules can be assigned to a processor. Does it mean that there is no way to start PD parallel simulations of whole protein? In other words, does it means that there is no way to run parallel simulation of protein in vacuum? You can do it the way all the other programs do: only use constraints on bonds involving H, and reducing the timestep to 1 fs. I try to run MD with only constrained h-bonds (constraints = hbonds) which allow 2fs timestep. The timestep 1fs would be needed if there will be vibrating (unconstrained) h-bonds. But you suggest to use constraints or it was a misprint? This is subject to discussion, see e.g. gromacs manual. Actually, with all bonds constrained 2 fs is already a large time step, and with only bonds containing H constrained 1 fs is also quite large. A further discussion can be found in the P-Lincs paper IIRC (J. Chem. Theor. Comp. 4 (2008) p. 116). Thank you for the reference. The subject is what I would like to know in more details. Regarding the problem that Shake block crossing node boundaries, the -load option implemented in gromacs-3.3.3 seems to remain the most computationally efficient due to the larger, at least technically, 2fs timestep. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in simulation of DMPC lipid bilayer
Mark Abraham wrote: nitu sharma wrote: Dear all, I am using DMPC lipid bilayer from teleman sir website to insert my protein in this lipid bilayer .I have done this by using command genbox. After that when I have run the command - pdb2gmx -f tap-in-dmpc.pdb -o tap-in-dmpc.gro -p tap-in-dmpc.top -i tap-in-dmpc-itp -ff oplsaa Error like this- There are 0 hydrogen bonds Warning: 'DMP' not found in residue topology database, trying to use 'DMSO' --- Program pdb2gmx, VERSION 4.0.3 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom C1 in residue DMSO 1 not found in rtp entry with 10 atoms while sorting atoms --- so please tell me how can I add DMP in residue topology database if anyone has knowledge about this. And please if also u know about any site of lipid bilayer from where i can download lipid bilayer then let me know. You may find some helpful information http://wiki.gromacs.org/index.php/Membrane_Simulations and http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database In addition to the above, which provide excellent background reference, consult the list archives for more stepwise instructions. What you will need to do is run pdb2gmx on *only* your protein, then modify the resulting topology to include parameters for dmpc. Again, the archive documents how to do this, it just takes some patience and persistence to find the right information. -Justin Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pulling of molecule in GROMACS 4.03
Dear Sir, I want to pull a molecule called PRO from the lipid membrane DPP. To do this I have written the .mdp file as following from the help of gromacs mannual 4.0 . But when I try to make .tpr file from the .gro file, it says that segmentation fault. Can you please write the correct .mdp file for the pulling? It will be really a great help to me. Thanking you, Anirban ; ; File 'mdout.mdp' was generated ; By user: psn (17109) ; On host: p690k ; At date: Fri Jul 23 12:43:31 2004 ; ; VARIOUS PREPROCESSING OPTIONS = title= lipid bilayer in water cpp = /lib/cpp include = define = ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 500 dt = 0.002 nsteps = 175 ; mode for center of mass motion removal = comm-mode= Linear ; number of steps for center of mass motion removal = nstcomm = 1 ; group(s) for center of mass motion removal = comm-grps= ; LANGEVIN DYNAMICS OPTIONS = ; Temperature, friction coefficient (amu/ps) and random seed = ;bd-temp = 300 ;I have commute the above line as it has no exitance bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells = niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints = fcstep = 0 ; Frequency of steepest descents steps when doing CG = nstcgsteep = 1000 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 250 nstenergy= 250 ; Output frequency and precision for xtc file = nstxtcout= 0 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or no = pbc = xyz ; nblist cut-off = rlist= 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME ;Reaction-Field rcoulomb-switch = 0 rcoulomb = 1.0 ;2.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 80.0 epsilon_rf = 1 ;I have done some thing new according to mannual and warnings and error ; Method for doing Van der Waals = vdwtype = Cut-off ; cut-off lengths= rvdw-switch = 0 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = Tcoupl = berendsen ; Groups to couple separately = tc-grps = DPP SOL PRO ; Time constant (ps) and reference temperature (K) = tau_t= 0.1 0.1 0.1 ref_t= 310 310 310 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 1.01.0 compressibility = 4.5e-5 4.5e-5 ref_p= 1.01.0 ; SIMULATED ANNEALING CONTROL = annealing= no ; Time at which temperature should be zero (ps) = ;zero-temp_time = 0 ;I have commute the above line as it has no exitance ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 310.0 gen_seed = 173529 ; OPTIONS FOR BONDS = constraints = all-bonds ; Type of constraint algorithm = constraint_algorithm = lincs ; Do not constrain the start configuration = continuation = yes ;unconstrained-start = no ; Use successive
[gmx-users] what factors effetc the simulation during energy minimization
hi.. I have been doing the simulation of protein which has 3 chains (trimer)and each chain with a length of 80 amino acids. I have done the simulation for 5ns. I have observed a sudden peak at 4ns so i continued simulating it to 10ns ..the peak which started at 4ns extended till 8ns .i have extracted the pdbs at this particular time frames.i found that the trimer is been spilt into monomer and dimer.i wanted to know exactly what are the parameters i need to adjust during the simulation to get a stabilised modelled structure. thanx Bhargavi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Explicit \ implicit
Hello Everyone, I always use gromacs for doing explicit simulations. I want to ask whether i can do the implicit simulations by using gromacs. Whether there is any tutorial or manual from which i can understand it better. If not, Then Pls tell me how to do it implicitly. With Regards Bhawana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Explicit \ implicit
Bhawana Gupta wrote: Hello Everyone, I always use gromacs for doing explicit simulations. I want to ask whether i can do the implicit simulations by using gromacs. Whether there is any tutorial or manual from which i can understand it better. If not, Then Pls tell me how to do it implicitly. implicit solvent willb e supported in 4.1 With Regards Bhawana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Explicit \ implicit
Bhawana Gupta wrote: Hello Everyone, I always use gromacs for doing explicit simulations. I want to ask whether i can do the implicit simulations by using gromacs. Whether there is any tutorial or manual from which i can understand it better. If not, Then Pls tell me how to do it implicitly. Did you start by searching the wiki? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] what factors effetc the simulation during energy minimization
bhargavi ch wrote: hi.. I have been doing the simulation of protein which has 3 chains (trimer)and each chain with a length of 80 amino acids. I have done the simulation for 5ns. I have observed a sudden peak at 4ns so i continued simulating it to 10ns ..the peak which started at 4ns extended till 8ns .i have extracted the pdbs at this particular time frames.i found that the trimer is been spilt into monomer and dimer.i wanted to know exactly what are the parameters i need to adjust during the simulation to get a stabilised modelled structure. Energy minimization does not occur over time, so you are mis-describing something here. You haven't told us what you're observing to peak at 4ns. Perhaps you need to understand some material here http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
hi.. I am working on the simulation of protein which has 3 chains (trimer)and each chain with a length of 80 amino acids. I have done the simulation for 5ns. I have observed a sudden shoot up in the RMS at 4ns so i continued simulating it to 10ns ..the peak which started at 4ns extended till 8ns .i have extracted the pdbs at this particular time frames.i found that the trimer is been spilt into monomer and dimer.i wanted to know exactly what are the parameters i need to adjust during the simulation to get a stabilised modelled structure. thanx Bhargavi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] what factors effetc the simulation during energy minimization
hi.. the sudden shoot up was observed in the RMS because of molecule breakage into monomer and dimer.we have also mutated some surface hydrophobic aminoacid and dint observe shoot up in any of the mutation. We have also observed the same shoot in the case of X ray crystallographic structure of template protein, when we did 10 ps simulation. what are the parameters which we need to take to avoid such shoot up?? thanx Bhargavi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] factors effecting the simulation
hi.. We were working on the simulation of protein which has 3 chains (trimer) and each chain with a length of 80 amino acids. We have done the simulation for 5ns.We have observed a sudden shoot up in the RMS at 4ns so we continued simulating it to 10ns .The peak which started at 4ns extended till 8ns because of molecule breakage into monomer and dimer. we have also mutated some surface hydrophobic amino acid and dint observe shoot up in any of the mutated simulations. We have also observed the same shoot in the case of X ray crystallographic structure of template protein, when we did it for 10 ps simulation. We have done position Restraint Dynamics for 100 ps. What are the parameters i need to adjust during the simulation to get a stabilized modeled structure?? Does the PR parameters have any effect on simulation?? thanx Bhargavi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] what factors effetc the simulation during energy minimization
bhargavi ch wrote: hi.. the sudden shoot up was observed in the RMS because of molecule breakage into monomer and dimer.we have also mutated some surface hydrophobic aminoacid and dint observe shoot up in any of the mutation. We have also observed the same shoot in the case of X ray crystallographic structure of template protein, when we did 10 ps simulation. what are the parameters which we need to take to avoid such shoot up?? As Mark pointed out, based on your original description, you are probably seeing PBC effects. Use trjconv to remove periodicity, and analyze the RMSD again. -Justin thanx Bhargavi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Calculation of fraction of native contacts
Dear users, I just started using GROMACS and have trouble figuring out an efficient way to compute the fraction of native contacts for a trajectory. I've checked available options such as g_mdmat, g_dist, g_hbond and g_mindist as well as previous posts, but still are not able to make a side-by-side comparison of the contacts of my reference protein structure with those of each frame in order to obtain the desired fraction. I would appreciate any help on this matter, Camilo ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Applying an improper to S-S bond
Hello, The question is not actually about S-S. I have a covalent bond between Cys (SG atom) ang Tyr (CE atom) residues. I`ve corrected the specbonds.dat and oplsaa topology to create a new residue (tyr2) and I use cys2 topology for cystein. During the MD the this covalent bond rotates a lot, so I think of applying an improper to the bond. The problem is that the fourth atom of a dihedral is always in another residue, I mean that I need the TYR2 CE atom to be present in CYS2 topology to set the improper and this is obviously impossible. 1/ How can I apply improper for this case? 2/ Any other (simpler) ways to freez the rotation? Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Using R.E.D. charges with OPLS AA
Hello, I need to simulate a protein with deprotonated Tyr (HH hydrogen should be off). I used R.E.D. approach with PCGAMESS and RESP to calculate the charges. 1/ The problem is that to my understanding RESP charges apply to AMBER only. Am I correct? 2/ Can I use R.E.D. charges with OPLS AA? 3/ If not how can I recalculate them to fit the OPLS AA? 4/ Any Tyr-Deprot topology already available??? Thanks, I appreciate your time. SDA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Applying an improper to S-S bond
DimitryASuplatov wrote: Hello, The question is not actually about S-S. I have a covalent bond between Cys (SG atom) ang Tyr (CE atom) residues. I`ve corrected the specbonds.dat and oplsaa topology to create a new residue (tyr2) and I use cys2 topology for cystein. During the MD the this covalent bond rotates a lot, so I think of applying an improper to the bond. The problem is that the fourth atom of a dihedral is always in another residue, I mean that I need the TYR2 CE atom to be present in CYS2 topology to set the improper and this is obviously impossible. 1/ How can I apply improper for this case? 2/ Any other (simpler) ways to freez the rotation? Probably a dihedral restraint is more appropriate. -Justin Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: Question for pulling in GROMACS 4.0
First of all it's best to post the error-message (i think there must be one). From the pulling options below i would say the problem is probably that you have 'pull_dim' and 'pull_geometry = direction', manual say 'pull_dim' is for 'distance' and 'position'. Another think is that you have in 'pull_vec1' 3 dimensions and in 'pull_init1' only one, this could be the problem when you used 'pull_geometry = position'. The last idea i have is this: 'pull_kB1 = 500'. The manual states that this is only for the free-energy-code. But this are only guesses, because we have no error-message and i have only used 'pull_dim = Y Y Y' with 'pull_geometry = position' (and that only once to try it out). Below are the options which i used (GROMACS 4.0.2) (the velocity and the force-constant are so high, that i see something in little time). REF and ZUG are single atoms, and the two vectors (pull_vec1, pull_init1) are the vector from REF to ZUG. I tried it also with 'pull_start = yes' and 'pull_init1 = 0.0 0.0 0.0' and it worked. But i never tried the other 'pull_geometry'-options. ; Pulling pull= umbrella pull_geometry = position pull_dim= Y Y Y pull_start = no pull_nstxout= 10 pull_nstfout= 10 pull_ngroups= 1 pull_group0 = REF pull_group1 = ZUG pull_vec1 = -0.012 -0.174 1.794 pull_init1 = -0.012 -0.174 1.794 pull_rate1 = 0.01 pull_k1 = 5000 -- Hope this helps Thomas == Dear Thomas, I took you name from the gromacs mail list. It seems that you have been successful using the pulling in the new gromacs version. I used the 3.3 version for simulating afm pulling but I could not do it with the new code. All I want to do is constant velocity pulling group r_76 in the Z direction. I tried pulling r_1 to 001 and r_76 00-1 using the option for pull_ngroups =2, tried pull_geometry = position and nothing worked. It's a simple protein with 76 residues and solvated in water. I am attaching at the end of the message my last try of pulling options I really appreciate any suggestion you may have on this matter. Thanks Marisa Roman Physics Dept. Drexel University, Philadelphia pull = umbrella pull_geometry = direction pull_start = yes pull_ngroups = 1 pull_group0 = r_1 pull_group1 = r_76 pull_dim = N N Y pull_start = yes pull_k1 = 500 pull_kB1 = 500 pull_rate1 = 0.05 pull_vec1 = 0 0 1 pull_init1 = 0.0 pull_nstxout = 100 pull_nstfout = 100 === ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Usually how do you decide the salt concentration?
Dear all, Usually how do you decide the salt concentration of the system? I got a protein structure from PDB, and what I am doing now is: to find out from which species the protein is extracted, and then search in google for the normal salt concentration of that species. However, it's hard to find the normal salt concentration. I will appreciate if you can share with me how you decide what the salt concentration. Thanks! Peggy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Usually how do you decide the salt concentration?
Peggy Yao wrote: Dear all, Usually how do you decide the salt concentration of the system? The salt concentration depends on a realistic physical model of whatever system you're examining. Note that in real biological systems, salt is a very broad, complex concept, so some approximations will have to be made. I got a protein structure from PDB, and what I am doing now is: to find out from which species the protein is extracted, and then search in google for the normal salt concentration of that species. However, it's hard to find the normal salt concentration. Well, then you've got your work cut out for you. Google is not the be-all end-all of information. Certainly there are studies using that particular organism, or at least some that are similar, about which more information is known. In the absence of information about the organism itself, search for whether or not assays have been performed on your protein that are involved in the behavior you hope to simulate. Those buffer conditions may be relevant to your simulations. -Justin I will appreciate if you can share with me how you decide what the salt concentration. Thanks! Peggy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Using R.E.D. charges with OPLS AA
DimitryASuplatov wrote: Hello, I need to simulate a protein with deprotonated Tyr (HH hydrogen should be off). I used R.E.D. approach with PCGAMESS and RESP to calculate the charges. 1/ The problem is that to my understanding RESP charges apply to AMBER only. Am I correct? 2/ Can I use R.E.D. charges with OPLS AA? 3/ If not how can I recalculate them to fit the OPLS AA? 4/ Any Tyr-Deprot topology already available??? http://wiki.gromacs.org/index.php/Parameterization Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Applying an improper to S-S bond
DimitryASuplatov wrote: Hello, The question is not actually about S-S. I have a covalent bond between Cys (SG atom) ang Tyr (CE atom) residues. I`ve corrected the specbonds.dat and oplsaa topology to create a new residue (tyr2) and I use cys2 topology for cystein. During the MD the this covalent bond rotates a lot, so I think of applying an improper to the bond. The problem is that the fourth atom of a dihedral is always in another residue, I mean that I need the TYR2 CE atom to be present in CYS2 topology to set the improper and this is obviously impossible. 1/ How can I apply improper for this case? Read and understand the relevant bits of chapters 4 5 of the manual, and add some suitable function to the .top file by hand. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to calculate PMF after AFM pulling
Hello everybody, I have recently run a SMD with AFM method, and i got the .pdo file. But i don't know how to use the .pdo file to calculate the PMF profile. Could someone give me some suggestion? Thanks a lot. Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
