[gmx-users] *.ITP file
Dear Users, I am trying to generate an *.ITP file for a ligand I am studying using Prodrg server. but the DRGPOH.PDB it gives to me displays only 26 atoms ( with apolar hydrogens) while the *.ITP file dispays 37 atoms and it does not display the double bond in the structure, which results in an error in simulation. Other files that Prodrg gives like DRGAPH.PDB display 37 atoms same as the *.ITP file and they also do not display the double bond in the structure ! only the DRGFIN.PDB with 41 atoms ( all hydrogens) displays the double bond. I have used Prodrg several times before and this is the first time it happens. are there any other online services or any software for the purpose? Thank you-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Spherical shaped box
Dear users, I am doing Protein Ligand simulation, increasing temp. from 100, 200, to 300 K. after 1ns of simulation in 300 K, the protein jumps out of the box and when I use the command trjconv_mpi -f *.trr -s *.tpr -o *new.trr -pbc nojump followed by trjconv_mpi -f new*.trr -s *.tpr -o new*.pdb -dump 1000 the box shape changes from dodecahedron to spherical. In Gromacs manual I read ; There are several possible shapes for space-filling unit cells. Some, as the rhombic dodecahedron and the truncated octahedron approach a spherical shape better than a cubic box and are therefore more economical for studying an (approximately spherical) macromolecule in solution, since less solvent molecules are required to fill the box given a minimum distance between macromolecular images... . Does it mean that it is ok and I can continue the simulation or I have to increase the box size? After simulation in 200 K the protein juped out of the box but using the same command the problem was fixed, without changing the box shape. Thank you in advance for the help Sogol-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Spherical shaped box
Dear Tsjerk Thank you Sogol From: Tsjerk Wassenaar tsje...@gmail.com To: Kowsar Bagherzadeh kw_bagherza...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, May 16, 2012 2:46 PM Subject: Re: [gmx-users] Spherical shaped box Hi Sogol, You remove jumps over periodic boundary conditions, giving a continuous trajectory. That gives you a very nice view on diffusion in your system, which happens to be equal in all directions. Hence, the end result looks spherical. But that's not the same as having a spherical box. If you draw the box in VMD or Pymol, you'll see it's still close to the original (triclinic) shape, but has become a bit small in relation to your molecules. Cheers, Tsjerk On Wed, May 16, 2012 at 11:49 AM, Kowsar Bagherzadeh kw_bagherza...@yahoo.com wrote: Dear users, I am doing Protein Ligand simulation, increasing temp. from 100, 200, to 300 K. after 1ns of simulation in 300 K, the protein jumps out of the box and when I use the command trjconv_mpi -f *.trr -s *.tpr -o *new.trr -pbc nojump followed by trjconv_mpi -f new*.trr -s *.tpr -o new*.pdb -dump 1000 the box shape changes from dodecahedron to spherical. In Gromacs manual I read ; There are several possible shapes for space-filling unit cells. Some, as the rhombic dodecahedron and the truncated octahedron approach a spherical shape better than a cubic box and are therefore more economical for studying an (approximately spherical) macromolecule in solution, since less solvent molecules are required to fill the box given a minimum distance between macromolecular images... . Does it mean that it is ok and I can continue the simulation or I have to increase the box size? After simulation in 200 K the protein juped out of the box but using the same command the problem was fixed, without changing the box shape. Thank you in advance for the help Sogol -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_rms -bm
Dear Users, I am trying to analyze a ligand-protein simulation results. I read in the manual that using g_rms command with –bm option produces a matrix of average bond angle deviations. And only bonds between atoms in the comparison groups are considered. Does it mean that it is for the bonds and their angles that are already in existence? (Not the ones that may be formed throughout simulation, I mean the ligand may for example interact with residues through H-bonds) .I have made a group in my index file named Active site (including only the active site residues), and I have a LIG group as well. If I choose these two groups for g_rms with this command: g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx Does it show me how the ligand affects the active site residues bond angles? And one more question, how can I study the ligand orientation in the active site? Sogol-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_rms -bm
Dear Users, I am trying to analyze a ligand-protein simulation results. I read in the manual that using g_rms command with –bm option produces a matrix of average bond angle deviations. And only bonds between atoms in the comparison groups are considered. Does it mean that it is for the bonds and their angles that are already in existence? (Not the ones that may be formed throughout simulation, I mean the ligand may for example interact with residues through H-bonds) .I have made a group in my index file named Active site (including only the active site residues), and I have a LIG group as well. If I choose these two groups for g_rms with this command: g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx Does it show me how the ligand affects the active site residues bond angles? And one more question, how can I study the ligand orientation in the active site? Sogol-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_rms -bm
Dear Justin Thank you very muchh Sogol From: Justin A. Lemkul jalem...@vt.edu To: Kowsar Bagherzadeh kw_bagherza...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, May 24, 2012 9:59 AM Subject: Re: [gmx-users] g_rms -bm On 5/24/12 7:24 AM, Kowsar Bagherzadeh wrote: Dear Users, I am trying to analyze a ligand-protein simulation results. I read in the manual that using g_rms command with –bm option produces a matrix of average bond angle deviations. And only bonds between atoms in the comparison groups are considered. Does it mean that it is for the bonds and their angles that are already in existence? (Not the ones that may be formed throughout simulation, I mean the ligand may for example interact with residues through H-bonds) .I have In this context, a bond means an actual chemical bond. A hydrogen bond is a nonbonded interaction. made a group in my index file named Active site (including only the active site residues), and I have a LIG group as well. If I choose these two groups for g_rms with this command: /g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx**/ Does it show me how the ligand affects the active site residues bond angles? Potentially. And one more question, how can I study the ligand orientation in the active site? That depends on how you define orientation - internal metrics like dihedrals or angles between planes of groups in the ligand, relative measurements like its position with respect to protein residues, etc. All analysis tools are listed in the manual, Chapter 8 and Appendix D. It's quite a lot to read, but you'll be able to identify all the various things you can analyze and how the information might be connected across different analysis routines. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] comparing simulations with diffrent forcefields
Dear Justin, Thank you very much for the reply Sogol From: Justin A. Lemkul jalem...@vt.edu To: Kowsar Bagherzadeh kw_bagherza...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, May 28, 2012 6:06 PM Subject: Re: [gmx-users] comparing simulations with diffrent forcefields On 5/28/12 7:07 AM, Kowsar Bagherzadeh wrote: Dear users, I have done a Ligand-Protein Simulation using 43a1.ff forcefield and ssDNA-Protein (the same protein I used for ligand protein simulation) using amber99sd-ILDN forcefield. Is it possible to compare the results of the two simulation with eachother? No? Maybe it's possible, but there will be a lot of caveats to the results. You may know of some intrinsic limitations or benefits of each force field that may explain away discrepancies, but the real complication comes with the ligand. How did you generate its parameters? Do you know exactly how those parameters will affect the local dynamics of the residues in which it makes contact? Do you know the equivalent result using a suitable Amber force field? If the answer to any of these questions is no, you'll have a hard time convincing a reviewer that your comparison is very meaningful. Net result: choose a force field, and use it for all simulations you wish to compare. It is substantially easier than trying to wiggle your way into a potentially incomplete or incorrect interpretation of the results. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] MD continuation
Hi, if you want to continue the simulation, you'd better use tpbconv command to generate a new *.tpr, or if you are using grompp command you have also to have -c previouse.tpr in the command line, there is no need for *.gro or *.top. From: delara aghaie d_agh...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, June 11, 2012 9:13 AM Subject: [gmx-users] MD continuation Hello I want to make sure about the command that I use. I have MD result for protein simulation MD for 1 ns. I want to continue this simulation for longer time. Check point file should be used for continuation: grompp -f md.mdp -c md-out.gro -t md.cpt -p topol.top -o md_2.tpr ** md-out.gro is the latest coordinate file that I have after 1 ns MD simulation ** md.cpt is the output of 1 ns simulation Is this command line enough to get the appropriate run input file for continuation? Thanks for your time D.M -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] hi
hey have a look http://www.com-im6.net/finance/ Kowsar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] box changes its shape !
Dear gmx-users, Running MD, I faced a problem, after 1ps of modeling, the box changes its shape from dodecahedron to rhomboid cube! and as a result some parts of the protein gets out of the box. I fixed it with trjcon command but keep comming up. Would you mind telling me where this problem arise from?! Sogol-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] problem with volume equilibration
You'd better first your .top file, to see if you have included DPPC .itp file and also in the compound section. if it was ok, check the .ndx and look for the atom numbers of DPPC, after finding the atom numbers, make a group ( Like othe parts of .ndx; water, or protein,...) and name it DPPC. save and continue. Hope it help Sogol From: Anushree Tripathi anushritripa...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, January 31, 2012 9:44 AM Subject: [gmx-users] problem with volume equilibration When I run the command (i.e., grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr)for volume equilibration. I am getting the error: Fatal error: Group DPPC not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Please guide me. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] problem with making index.ndx
Is DPPC a ligand or a compound ? From: Anushree Tripathi anushritripa...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, January 31, 2012 10:56 AM Subject: [gmx-users] problem with making index.ndx I am using gromacs 4.5.3 version.When I run the command (i.e., make_ndx -f em.gro -o index.ndx),It is not showing any option for DPPC group which I want to include.Please tell me how could I merge or create this option for proceeding to the next step of NVT simulation. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] problem with make_ndx
You should first make an *.itp file for DPPC, then include it in the *.top file. whatever that is not in GROMACS library should be defined to it. You would better see http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf , hope it will help. From: Anushree Tripathi anushritripa...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, February 1, 2012 10:34 AM Subject: [gmx-users] problem with make_ndx When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is showing the following options: 0 System : 18379 atoms 1 Protein : 11739 atoms 2 Protein-H : 9135 atoms 3 C-alpha : 1173 atoms 4 Backbone : 3519 atoms 5 MainChain : 4693 atoms 6 MainChain+Cb : 5773 atoms 7 MainChain+H : 5842 atoms 8 SideChain : 5897 atoms 9 SideChain-H : 4442 atoms 10 Prot-Masses : 11739 atoms 11 non-Protein : 6640 atoms 12 Water : 6636 atoms 13 SOL : 6636 atoms 14 non-Water : 11743 atoms 15 Ion : 4 atoms 16 CL : 4 atoms 17 Water_and_ions : 6640 atoms for my work, I used 16|13 then 1|11.lastly I saved it using 'q'.But there is no option for DPPC (as given in tutorial we have to merge protein with DPPC).After runing the command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),it is showing error: Group DPPC not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. To troubleshoot the error,I have kept one more group in index.ndx file with number of atoms which I found from dppc.itp file(at the end of file) like this [DPPC] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 Again after running the grompp command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),I am getting the following error: Atom 1 in multiple T-Coupling groups (1 and 2). Please suggest me the reason as well as solution for this problem. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
