[gmx-users] required topology stuff modification for GBSA
Dear GROMACS users: This is self-reply to resolve the following error I'd met. Then I believe the error Fatal error: Cannot find length for atoms 1-3 involved in angle. occurs with some side-effects from the implicit solvent setting. I'd found that the topology stuff should be more strictly written with implicit_solvent=GBSA than that with implicit_solvent=no. For simple example, all-atom CH4 molecule has five atoms and four bonds and six angles. If I only have five angles by mistake, it is tolerant with implicit_solvent=no but result in the error above with implicit_solvent=GBSA. It means you should check the number of angles, if you've got the error when you change implicit_solvent=no to implicit_solvent=GBSA. Hope it helps. Regards, Makoto Yoneya, Dr. http://staff.aist.go.jp/makoto-yoneya/ -- 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] Re: About the %SS values in the output of do_dssp
Ok Thank you Justin for this clarification
sa wrote:
Dear All,
I have simulated 6 peptides (with 7 AA each capped in N and C termini)
in water and trehalose. During all the simulation time, the six peptides
have b-sheet conformations. I would like to calculate the average % of
secondary structure for the 6 peptides over the course of run. So I have
read the subject reported in the following link
http://redmine.gromacs.org/issues/683 and used the following command for
the two first frames
/work/sa001/gmx-post4.5.3/bin/do_dssp_mpi -f *-Center_All.xtc -s
run_1.tpr -tu ps -dt 1 -b 1 -e 5 -o
6_Peptide_53A6_Trehal_Pref_SS.xpm -sss
6_Peptide_53A6_Trehal_Pref_HEBT.dat -ssdump
6_Peptide_53A6_Trehal_Dump_SS.dat -sc test.xvg
I obtained the following output for my six peptides
@TYPE xy
@ subtitle Structure = + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + B-Sheet + + + + + +
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend Structure
@ s1 legend Coil
@ s2 legend B-Sheet
@ s3 legend Chain_Separator
2301230 5
4301230 5
# Totals60246010
# SS %0.64 0.26 0.64 0.11
I can understand how the %SS values are obtained in the example given in
http://redmine.gromacs.org/issues/683, but not in my case. Could you
tell me how the %SS is obtained the output above.
Like any other average. From the code:
/* now print percentages */
fprintf(fp, %-8s %5.2f, # SS %, total_count / (real) (mat-nx *
mat-ny));
for(s=0; smat-nmap; s++)
{
fprintf(fp, %5.2f,total[s] / (real) (mat-nx * mat-ny));
}
fprintf(fp,\n);
So the total number of secondary structure elements is divided by the
product of
(number of frames * number of total residues).
Your results are affected by the problem I mentioned in the issue report
you
quote. You have 42 residues, but since chain separators count as residues,
the
calculations are all done out of 47 residues instead. You'll have to
either
modify the code to account for this problem or simply re-calculate the
averages
yourself.
-Justin
Thank you in advance for your help
SA
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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[gmx-users] R: gmx-users Digest, Vol 86, Issue 183
Dear Tsjerk, dear all, thank you very much for suggestion. One of the main reasons why I never used the rhombic dodecahedron box for my simulations is the fact that it is really hard to visualize the results with programs such as VMD or Pymol, and therefore I cannot check easily during the setting of my system if the work proceeds properly. Since I would like to redo my simulations following your suggestion, could you please give me some hints on how to proceed in order to visualize easily the system? For example, now I created a dodecahedric box filled with water and ions. I tried to visualize it with VMD and I saw it as a rectangular box with the protein at one edge. I tried to use the command trjconv: trjconv -f prot_dod_box_neu.gro -s prot_dod_box_neu.tpr -o prot_dod_box_neu2.gro -pbc mol -ur compact and I obtained an error message stating: Fatal error: Index[84328] 84329 is larger than the number of atoms in the trajectory file (84328) I don't find this error neither in the gmx-users list archive (indeed it's becoming harder and harder to search into this archive, given that each message is visualized 10 times, as I already noticed sometimes ago), nor in the Error section. The first .gro file is the one coming from genion, and the .tpr file is the one I used to neutralize the system, which is the .tpr file I should give to trjconv? You see, if every time I try to use a box different from the standard cubic one I has to deal with such maybe trivial (for you) problems, but difficult and long to solve, I'm quite discouraged to use it! This is also a kind request for Gromacs Web site managers: could you please add a section for this (recurrent, I suspect) problem of box visualization in the How-to section? it would be very useful for users, I think, and probably also for you (less trivial questions posted to the gmx-users list...) Many thanks in advance for the help you could provide me. Anna Message: 6 Date: Mon, 27 Jun 2011 17:05:17 +0200 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] about periodic images violation To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: banlktim3r1339yb6eckedf9etyrg+q+...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Anna, The spikes you see occur because the protein is broken over the periodic boundaries. Not hard to see that a broken molecule will have a minimal minimal distance. The other problem may well occur due to rotation of your molecule. Since you set -bt tric, you just get a rectangular unit cell, which has the drawback that the shortest distance may not be long enough to keep the protein from self-interactions in certain orientations. I know it's considered a pretty standard setup, which is why I mentioned it before. You should use a rhombic dodecahedron. With a rectangular cell, you could even have self-interaction in a nastier way: the ends of the protein can try to avoid each other, rather than align with each other. That would result in an altered ensemble, yet one in which you wouldn't see violations of the minimal distance. In a rhombic dodecahedron the spatial distribution is much more uniform... Cheers, Tsjerk On Mon, Jun 27, 2011 at 12:48 PM, Anna Marabotti anna.marabo...@isa.cnr.it wrote: Dear gmx-users, I'm inserting into the discussion about periodic images since I'm experimenting a problem of minimum distance violation too. I'm doing simulations on a dimeric protein (with no covalent bonds between the two subunits) which derives not from a crystallographic structure but from a model. I made several simulations changing the gen_seed in order to explore deeply the conformational space of the protein. I used a triclinic box (option editconf -bt triclinic -d 1 -c) filled with spc water and neutralized with ions; in my opinion, it's quite a standard system. I equilibrated the system with a minimization (emtol = 500 reached) and with NVT+NPT in position-restrained mode (20+100 ps) at 310 K, then launched the full MD for 30 ns, always at 310 K. I repeated this procedure (NVT+NPT+FullMD) for each of the gen_seed assigned (random numbers), starting from the same minimized structure. Obviously, in PR-NPT and full Md simulations, I did not recalculated the initial velocity (it's a continuation). Before starting with full MD I checked for energetic parameters in .edr file (Pot, Kin, Tot, T, P) and all seem stable with no apparent problems. I run the 30 ns simulations and now I'm checking for the results. Looking at the trajectories I see that in some (but not all) cases, the protein moves from the center of the box to one of the edges, starting from a time that is different in each simulation, when it happens. I run g_mindist, and in some cases (generally when the protein doesn't move so much) I see some spikes in the plot (that disappear if I apply trjconv -pbc nojump to the trajectory), but apart from these spikes the minimum periodic distance in the trajectory is
[gmx-users] about periodic image violations
Sorry, I forgot to change the subject of my previous mail. Anna -Messaggio originale- Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] Inviato: martedì 28 giugno 2011 12.09 A: 'gmx-users@gromacs.org' Oggetto: R: gmx-users Digest, Vol 86, Issue 183 Dear Tsjerk, dear all, thank you very much for suggestion. One of the main reasons why I never used the rhombic dodecahedron box for my simulations is the fact that it is really hard to visualize the results with programs such as VMD or Pymol, and therefore I cannot check easily during the setting of my system if the work proceeds properly. Since I would like to redo my simulations following your suggestion, could you please give me some hints on how to proceed in order to visualize easily the system? For example, now I created a dodecahedric box filled with water and ions. I tried to visualize it with VMD and I saw it as a rectangular box with the protein at one edge. I tried to use the command trjconv: trjconv -f prot_dod_box_neu.gro -s prot_dod_box_neu.tpr -o prot_dod_box_neu2.gro -pbc mol -ur compact and I obtained an error message stating: Fatal error: Index[84328] 84329 is larger than the number of atoms in the trajectory file (84328) I don't find this error neither in the gmx-users list archive (indeed it's becoming harder and harder to search into this archive, given that each message is visualized 10 times, as I already noticed sometimes ago), nor in the Error section. The first .gro file is the one coming from genion, and the .tpr file is the one I used to neutralize the system, which is the .tpr file I should give to trjconv? You see, if every time I try to use a box different from the standard cubic one I has to deal with such maybe trivial (for you) problems, but difficult and long to solve, I'm quite discouraged to use it! This is also a kind request for Gromacs Web site managers: could you please add a section for this (recurrent, I suspect) problem of box visualization in the How-to section? it would be very useful for users, I think, and probably also for you (less trivial questions posted to the gmx-users list...) Many thanks in advance for the help you could provide me. Anna Message: 6 Date: Mon, 27 Jun 2011 17:05:17 +0200 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] about periodic images violation To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: banlktim3r1339yb6eckedf9etyrg+q+...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Anna, The spikes you see occur because the protein is broken over the periodic boundaries. Not hard to see that a broken molecule will have a minimal minimal distance. The other problem may well occur due to rotation of your molecule. Since you set -bt tric, you just get a rectangular unit cell, which has the drawback that the shortest distance may not be long enough to keep the protein from self-interactions in certain orientations. I know it's considered a pretty standard setup, which is why I mentioned it before. You should use a rhombic dodecahedron. With a rectangular cell, you could even have self-interaction in a nastier way: the ends of the protein can try to avoid each other, rather than align with each other. That would result in an altered ensemble, yet one in which you wouldn't see violations of the minimal distance. In a rhombic dodecahedron the spatial distribution is much more uniform... Cheers, Tsjerk On Mon, Jun 27, 2011 at 12:48 PM, Anna Marabotti anna.marabo...@isa.cnr.it wrote: Dear gmx-users, I'm inserting into the discussion about periodic images since I'm experimenting a problem of minimum distance violation too. I'm doing simulations on a dimeric protein (with no covalent bonds between the two subunits) which derives not from a crystallographic structure but from a model. I made several simulations changing the gen_seed in order to explore deeply the conformational space of the protein. I used a triclinic box (option editconf -bt triclinic -d 1 -c) filled with spc water and neutralized with ions; in my opinion, it's quite a standard system. I equilibrated the system with a minimization (emtol = 500 reached) and with NVT+NPT in position-restrained mode (20+100 ps) at 310 K, then launched the full MD for 30 ns, always at 310 K. I repeated this procedure (NVT+NPT+FullMD) for each of the gen_seed assigned (random numbers), starting from the same minimized structure. Obviously, in PR-NPT and full Md simulations, I did not recalculated the initial velocity (it's a continuation). Before starting with full MD I checked for energetic parameters in .edr file (Pot, Kin, Tot, T, P) and all seem stable with no apparent problems. I run the 30 ns simulations and now I'm checking for the results. Looking at the trajectories I see that in some (but not all) cases, the protein moves from the center of the box to one of the edges, starting from a time that is different in each simulation, when it happens.
[gmx-users] Broken protein chain.
Dear users, Has anyone done simulation with a broken crystal structure? I know that it can be modeled before simulating. But I just wanted to know whether any one had done with the crystal structure having breakage as such without modelling. Thanking you Respectfully M. Kavyashree -- 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] Tabulated potential for metal-oxide
Dear All,
I've just started using GROMACS, I've read the manual and searched the
mailing list but still confused. I'm trying to simulate metal oxidation with
GROMACS. As a first step, I'm trying to tabulate the EAM (Embedded atom
potential), which in addition to residual pair-pair repulsion includes the
energy required to embed atom i in a local electron density rho, where rho
is defined as:
rho_i=SUM{k_j*exp(-beta_j*(r_ij-r*_j)) }
k, beta, r*_j are known parameters and the sum runs over all other atoms.
Is there any way to tabulate the energy functional of such local electron
density?
Manana
Post-graduate student,
Aalto University, School of Science
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Re: [gmx-users] about periodic image violations
Anna Marabotti wrote: Sorry, I forgot to change the subject of my previous mail. Anna -Messaggio originale- Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] Inviato: martedì 28 giugno 2011 12.09 A: 'gmx-users@gromacs.org' Oggetto: R: gmx-users Digest, Vol 86, Issue 183 Dear Tsjerk, dear all, thank you very much for suggestion. One of the main reasons why I never used the rhombic dodecahedron box for my simulations is the fact that it is really hard to visualize the results with programs such as VMD or Pymol, and therefore I cannot check easily during the setting of my system if the work proceeds properly. Since I would like to redo my simulations following your suggestion, could you please give me some hints on how to proceed in order to visualize easily the system? For example, now I created a dodecahedric box filled with water and ions. I tried to visualize it with VMD and I saw it as a rectangular box with the protein at one edge. I tried to use the command trjconv: trjconv -f prot_dod_box_neu.gro -s prot_dod_box_neu.tpr -o prot_dod_box_neu2.gro -pbc mol -ur compact and I obtained an error message stating: Fatal error: Index[84328] 84329 is larger than the number of atoms in the trajectory file (84328) I don't find this error neither in the gmx-users list archive (indeed it's becoming harder and harder to search into this archive, given that each message is visualized 10 times, as I already noticed sometimes ago), nor in the Error section. The first .gro file is the one coming from genion, and the .tpr file is the one I used to neutralize the system, which is the .tpr file I should give to trjconv? You see, if every time I try to use a box They need to correspond to the same system. Therefore, after the system is constructed (i.e. after genion in this case), create a new .tpr file. Your command is otherwise correct. Whether or not VMD then displays the proper unit cell shape is another matter. If you display all of the solvent molecules, you should get a nice, pseudo-spherical shape, but if you visualize the box vectors then I think you'll still get a triclinic cell. But that's a VMD thing, not a Gromacs thing :) -Justin different from the standard cubic one I has to deal with such maybe trivial (for you) problems, but difficult and long to solve, I'm quite discouraged to use it! This is also a kind request for Gromacs Web site managers: could you please add a section for this (recurrent, I suspect) problem of box visualization in the How-to section? it would be very useful for users, I think, and probably also for you (less trivial questions posted to the gmx-users list...) Many thanks in advance for the help you could provide me. Anna Message: 6 Date: Mon, 27 Jun 2011 17:05:17 +0200 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] about periodic images violation To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: banlktim3r1339yb6eckedf9etyrg+q+...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Anna, The spikes you see occur because the protein is broken over the periodic boundaries. Not hard to see that a broken molecule will have a minimal minimal distance. The other problem may well occur due to rotation of your molecule. Since you set -bt tric, you just get a rectangular unit cell, which has the drawback that the shortest distance may not be long enough to keep the protein from self-interactions in certain orientations. I know it's considered a pretty standard setup, which is why I mentioned it before. You should use a rhombic dodecahedron. With a rectangular cell, you could even have self-interaction in a nastier way: the ends of the protein can try to avoid each other, rather than align with each other. That would result in an altered ensemble, yet one in which you wouldn't see violations of the minimal distance. In a rhombic dodecahedron the spatial distribution is much more uniform... Cheers, Tsjerk On Mon, Jun 27, 2011 at 12:48 PM, Anna Marabotti anna.marabo...@isa.cnr.it wrote: Dear gmx-users, I'm inserting into the discussion about periodic images since I'm experimenting a problem of minimum distance violation too. I'm doing simulations on a dimeric protein (with no covalent bonds between the two subunits) which derives not from a crystallographic structure but from a model. I made several simulations changing the gen_seed in order to explore deeply the conformational space of the protein. I used a triclinic box (option editconf -bt triclinic -d 1 -c) filled with spc water and neutralized with ions; in my opinion, it's quite a standard system. I equilibrated the system with a minimization (emtol = 500 reached) and with NVT+NPT in position-restrained mode (20+100 ps) at 310 K, then launched the full MD for 30 ns, always at 310 K. I repeated this procedure (NVT+NPT+FullMD) for each of the gen_seed assigned (random numbers), starting from the same minimized structure. Obviously, in
Re: [gmx-users] Broken protein chain.
Kavyashree M wrote: Dear users, Has anyone done simulation with a broken crystal structure? I know that it can be modeled before simulating. But I just wanted to know whether any one had done with the crystal structure having breakage as such without modelling. You need an intact starting structure to create a reasonable topology and run any sort of simulation. Missing termini may not be significant, but any atoms or residues missing within the chain have to be reconstructed. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Broken protein chain.
Sir, Ok Thanks. With Regards M. Kavyashree On Tue, Jun 28, 2011 at 4:25 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Dear users, Has anyone done simulation with a broken crystal structure? I know that it can be modeled before simulating. But I just wanted to know whether any one had done with the crystal structure having breakage as such without modelling. You need an intact starting structure to create a reasonable topology and run any sort of simulation. Missing termini may not be significant, but any atoms or residues missing within the chain have to be reconstructed. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] force on protein by solvent
Dear all, I want to calculate the force on each protein atom induced by the SPC solvent. Therefore I use the mdrun -rerun option and add to the .mdp file the line energygrps = Protein SOL If I compare afterwards the total force and the force of the solvent written to the trr file I get for the second one absolute values which are up to two times bigger when the total forces (including all the protein protein forces). I do not think that cancellations of inter and intra molecular forces should have such a big impact. Without the energygrps the rerun gives the same values as the original run. So I am not sure if it is enough to just add the above line to the .mdp file before doing the restart. Any help is welcomed Thanks Basti -- 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] Tabulated potential for metal-oxide
On 28/06/2011 8:49 PM, manana koberidze wrote:
Dear All,
I've just started using GROMACS, I've read the manual and searched the
mailing list but still confused. I'm trying to simulate metal
oxidation with GROMACS. As a first step, I'm trying to tabulate the
EAM (Embedded atom potential), which in addition to residual pair-pair
repulsion includes the energy required to embed atom i in a local
electron density rho, where rho is defined as:
rho_i=SUM{k_j*exp(-beta_j*(r_ij-r*_j)) }
k, beta, r*_j are known parameters and the sum runs over all other atoms.
Is there any way to tabulate the energy functional of such local
electron density?
Since it depends only on inter-atomic coordinates, it should be
possible. Before that, get some experience with normal GROMACS simulations.
Mark
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Re: [gmx-users] gromacs 2.1
On Sun, Jun 26, 2011 at 14:09, chris.ne...@utoronto.ca wrote: /bin/sh: line 0: cd: include: No such file or directory There's a mistake in the Makefile: include is one level higher, but is treated as if it would be in the current level and a cd .. is done afterwards. You can move include into src, or just add a link to it: cd src ln -s ../include . dlist.c:197:1: error: pasting . and H does not give a valid preprocessing token A similar error appears for me also for src/kernel/tpbcmp.c. In both cases, look up the corresponding lines and remove the pasting/concatenation operator ## as gcc seems to be smart and do what it's supposed to do even without it. F.e. the offending line in src/tools/dlist.c should look like: #define BBB(x) (dl-atm.x != -1) This is supported by several posts on the 'net, f.e.: http://groups.google.com/group/comp.lang.c.moderated/browse_thread/thread/33e7f5f44f25ca81 My tests were done on Fedora 14 with gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4). Good luck! Bogdan -- 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] reg ionic strngth
Dear justin, Thank you for your Previous Reply. Now I am studying The effect of ionic strength on the disassociation of My protein using steered MD . I would like to explain my result of pullf.xvg force profile variation for different concentration of ions . my Question is Which interaction factor Should i take for analysis to justify my force profile. Either H-bonding Interaction or HydroPhobic Interaction . Thanks in Advance -- 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] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27
Dear gromacs users, I constructed a small *.pdb file comprised of only lipids (POPE bilayer). If I try to convert this pdb file with pdb2gmx (gromacs 4.5.4) and the included charmm27 forcefield, I get warnings for missing hydrogen atoms and Long Bond warnings. In other threads, the lipids.hdb is discussed in this context. In my case, all hydrogen atoms are available. Do I need to proceed the lipids.hdb (like described in the manual), or can I leave it empty ? The resnames are consistent with the lipids.rtp entries. Thanks for all your help, M.Kalavera Additional information Command used: pdb2gmx_mpi -f lipids.pdb -p lipids.top -o lipids.gro -water TIP3P -ff charmm27 The first entries of my pdb file: REMARK ATOM 1 N POPE1 -14.135 -21.952 22.035 1.00 0.00 LIPI ATOM 2 HN1 POPE1 -14.125 -22.660 22.797 1.00 0.00 LIPI ATOM 3 HN2 POPE1 -13.175 -21.821 21.659 1.00 0.00 LIPI ATOM 4 HN3 POPE1 -14.339 -21.041 22.493 1.00 0.00 LIPI ATOM 5 C12 POPE1 -15.154 -22.312 21.033 1.00 0.00 LIPI ATOM 6 H12A POPE1 -16.107 -22.486 21.577 1.00 0.00 LIPI ATOM 7 H12B POPE1 -14.920 -23.252 20.489 1.00 0.00 LIPI ATOM 8 C11 POPE1 -15.234 -21.168 20.058 1.00 0.00 LIPI ATOM 9 H11A POPE1 -14.276 -20.976 19.529 1.00 0.00 LIPI ATOM 10 H11B POPE1 -15.909 -21.556 19.266 1.00 0.00 LIPI ATOM 11 P POPE1 -15.310 -18.486 20.024 1.00 0.00 LIPI ATOM 12 O13 POPE1 -16.549 -17.712 19.663 1.00 0.00 LIPI ATOM 13 O14 POPE1 -14.314 -17.846 20.940 1.00 0.00 LIPI ATOM 14 O11 POPE1 -14.637 -18.744 18.604 1.00 0.00 LIPI ATOM 15 O12 POPE1 -15.752 -19.947 20.557 1.00 0.00 LIPI ATOM 16 C1 POPE1 -14.267 -17.491 18.032 1.00 0.00 LIPI ATOM 17 HA POPE1 -15.110 -16.900 17.614 1.00 0.00 LIPI ATOM 18 HB POPE1 -13.690 -16.851 18.733 1.00 0.00 LIPI ATOM 19 C2 POPE1 -13.395 -17.725 16.681 1.00 0.00 LIPI ATOM 20 HS POPE1 -12.357 -17.976 16.987 1.00 0.00 LIPI ATOM 21 O21 POPE1 -13.383 -16.549 15.849 1.00 0.00 LIPI ATOM 22 C21 POPE1 -12.419 -16.414 14.956 1.00 0.00 LIPI ATOM 23 O22 POPE1 -11.405 -17.098 14.835 1.00 0.00 LIPI ATOM 24 C22 POPE1 -12.767 -15.262 13.918 1.00 0.00 LIPI ATOM 25 H2R POPE1 -13.659 -15.556 13.324 1.00 0.00 LIPI ATOM 26 H2S POPE1 -12.825 -14.275 14.427 1.00 0.00 LIPI ATOM 27 C3 POPE1 -13.924 -18.925 15.834 1.00 0.00 LIPI ATOM 28 HX POPE1 -13.196 -19.033 15.002 1.00 0.00 LIPI ATOM 29 HY POPE1 -13.829 -19.915 16.331 1.00 0.00 LIPI ATOM 30 O31 POPE1 -15.338 -18.716 15.377 1.00 0.00 LIPI ATOM 31 C31 POPE1 -15.514 -19.308 14.227 1.00 0.00 LIPI ATOM 32 O32 POPE1 -14.683 -19.825 13.544 1.00 0.00 LIPI ATOM 33 C32 POPE1 -17.023 -19.166 13.689 1.00 0.00 LIPI ATOM 34 H2X POPE1 -17.106 -20.050 13.022 1.00 0.00 LIPI ATOM 35 H2Y POPE1 -17.627 -19.380 14.597 1.00 0.00 LIPI ATOM 36 C23 POPE1 -11.614 -14.871 12.965 1.00 0.00 LIPI ATOM 37 H3R POPE1 -11.533 -13.767 12.868 1.00 0.00 LIPI ATOM 38 H3S POPE1 -10.669 -15.218 13.434 1.00 0.00 LIPI ATOM 39 C24 POPE1 -11.678 -15.385 11.524 1.00 0.00 LIPI ATOM 40 H4R POPE1 -12.586 -14.837 11.192 1.00 0.00 LIPI ATOM 41 H4S POPE1 -10.819 -15.050 10.904 1.00 0.00 LIPI ATOM 42 C25 POPE1 -12.001 -16.882 11.443 1.00 0.00 LIPI ATOM 43 H5R POPE1 -11.079 -17.466 11.651 1.00 0.00 LIPI ATOM 44 H5S POPE1 -12.770 -17.181 12.187 1.00 0.00 LIPI ATOM 45 C26 POPE1 -12.435 -17.332 10.094 1.00 0.00 LIPI ATOM 46 H6R POPE1 -12.808 -18.375 10.172 1.00 0.00 LIPI ATOM 47 H6S POPE1 -13.247 -16.723 9.640 1.00 0.00 LIPI ATOM 48 C27 POPE1 -11.179 -17.198 9.148 1.00 0.00 LIPI ATOM 49 H7R POPE1 -10.668 -16.220 9.280 1.00 0.00 LIPI ATOM 50 H7S POPE1 -10.407 -17.957 9.395 1.00 0.00 LIPI ATOM 51 C28 POPE1 -11.573 -17.384 7.605 1.00 0.00 LIPI ATOM 52 H8R POPE1 -12.256 -16.556 7.320 1.00 0.00 LIPI
[gmx-users] How to protonate a gmx trajectory?
Hi there, I am using GROMACS4.5.4 and the GROMOS 53A6 united-atom force field to do MD with my protein-ligand system. I was trying to add aliphatic hydrogens to the .gro and .trr or .xtc trajectory file with g_protonate, but the Fatal error was: Library file in current dir nor not found ffgmx2in defalt directories. Then re-name the directory in ../share/top/gmx2.ff to ffgmx2, and this time g_protonate seems to be able to find those .hdb files. But another error follows as: Reading frames from gro file 'Protein in water', 66743 atoms. Reading frame 0 time0.000 Opening force field file ffgmx2/aminoacids.hdb Opening force field file ffgmx2/atomtypes.atp Atomtype 1 Opening force field file ffgmx2/aminoacids.n.tdb Opening force field file ffgmx2/aminoacids.c.tdb Segmentation fault I searched for 'Segmentation fault', nothing relevant to g_protonate came up. So I wonder if anyone could kindly help me out? Or is there an easy alternative way to protonate the trajectory file? Thanks a lot for your attention. Yun -- 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] reg ionic strngth
vidhya sankar wrote: Dear justin, Thank you for your Previous Reply. Now I am studying The effect of ionic strength on the disassociation of My protein using steered MD . I would like to explain my result of pullf.xvg force profile variation for different concentration of ions . my Question is Which interaction factor Should i take for analysis to justify my force profile. Either H-bonding Interaction or HydroPhobic Interaction . I know nothing about the system you are working on, nor does anyone else on this list. If you have an inquiry about a Gromacs function, please post it, otherwise do not expect the users of this list to do your thinking for you. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27
kalav...@gmx.net wrote: Dear gromacs users, I constructed a small *.pdb file comprised of only lipids (POPE bilayer). If I try to convert this pdb file with pdb2gmx (gromacs 4.5.4) and the included charmm27 forcefield, I get warnings for missing hydrogen atoms and Long Bond warnings. pdb2gmx is ill-suited for dealing with multiple molecules. The better approach is to work with a single POPE molecule with a suitably constructed .rtp entry for it. pdb2gmx should then generate a topology for one lipid, which can then be modified to be used in an #include statement or extended to accommodate an entire bilayer simply by altering the [molecules] directive. The errors you are seeing are likely due to naming mismatch or poor starting geometry, but since you haven't quoted the errors, I don't dare guess beyond that. In other threads, the lipids.hdb is discussed in this context. In my case, all hydrogen atoms are available. Do I need to proceed the lipids.hdb (like described in the manual), or can I leave it empty ? The .hdb file is only necessary to reconstruct missing H atoms. If your structure has all of them and they are correctly named, then an .hdb is not necessary. -Justin The resnames are consistent with the lipids.rtp entries. Thanks for all your help, M.Kalavera Additional information Command used: pdb2gmx_mpi -f lipids.pdb -p lipids.top -o lipids.gro -water TIP3P -ff charmm27 The first entries of my pdb file: REMARK ATOM 1 N POPE1 -14.135 -21.952 22.035 1.00 0.00 LIPI ATOM 2 HN1 POPE1 -14.125 -22.660 22.797 1.00 0.00 LIPI ATOM 3 HN2 POPE1 -13.175 -21.821 21.659 1.00 0.00 LIPI ATOM 4 HN3 POPE1 -14.339 -21.041 22.493 1.00 0.00 LIPI ATOM 5 C12 POPE1 -15.154 -22.312 21.033 1.00 0.00 LIPI ATOM 6 H12A POPE1 -16.107 -22.486 21.577 1.00 0.00 LIPI ATOM 7 H12B POPE1 -14.920 -23.252 20.489 1.00 0.00 LIPI ATOM 8 C11 POPE1 -15.234 -21.168 20.058 1.00 0.00 LIPI ATOM 9 H11A POPE1 -14.276 -20.976 19.529 1.00 0.00 LIPI ATOM 10 H11B POPE1 -15.909 -21.556 19.266 1.00 0.00 LIPI ATOM 11 P POPE1 -15.310 -18.486 20.024 1.00 0.00 LIPI ATOM 12 O13 POPE1 -16.549 -17.712 19.663 1.00 0.00 LIPI ATOM 13 O14 POPE1 -14.314 -17.846 20.940 1.00 0.00 LIPI ATOM 14 O11 POPE1 -14.637 -18.744 18.604 1.00 0.00 LIPI ATOM 15 O12 POPE1 -15.752 -19.947 20.557 1.00 0.00 LIPI ATOM 16 C1 POPE1 -14.267 -17.491 18.032 1.00 0.00 LIPI ATOM 17 HA POPE1 -15.110 -16.900 17.614 1.00 0.00 LIPI ATOM 18 HB POPE1 -13.690 -16.851 18.733 1.00 0.00 LIPI ATOM 19 C2 POPE1 -13.395 -17.725 16.681 1.00 0.00 LIPI ATOM 20 HS POPE1 -12.357 -17.976 16.987 1.00 0.00 LIPI ATOM 21 O21 POPE1 -13.383 -16.549 15.849 1.00 0.00 LIPI ATOM 22 C21 POPE1 -12.419 -16.414 14.956 1.00 0.00 LIPI ATOM 23 O22 POPE1 -11.405 -17.098 14.835 1.00 0.00 LIPI ATOM 24 C22 POPE1 -12.767 -15.262 13.918 1.00 0.00 LIPI ATOM 25 H2R POPE1 -13.659 -15.556 13.324 1.00 0.00 LIPI ATOM 26 H2S POPE1 -12.825 -14.275 14.427 1.00 0.00 LIPI ATOM 27 C3 POPE1 -13.924 -18.925 15.834 1.00 0.00 LIPI ATOM 28 HX POPE1 -13.196 -19.033 15.002 1.00 0.00 LIPI ATOM 29 HY POPE1 -13.829 -19.915 16.331 1.00 0.00 LIPI ATOM 30 O31 POPE1 -15.338 -18.716 15.377 1.00 0.00 LIPI ATOM 31 C31 POPE1 -15.514 -19.308 14.227 1.00 0.00 LIPI ATOM 32 O32 POPE1 -14.683 -19.825 13.544 1.00 0.00 LIPI ATOM 33 C32 POPE1 -17.023 -19.166 13.689 1.00 0.00 LIPI ATOM 34 H2X POPE1 -17.106 -20.050 13.022 1.00 0.00 LIPI ATOM 35 H2Y POPE1 -17.627 -19.380 14.597 1.00 0.00 LIPI ATOM 36 C23 POPE1 -11.614 -14.871 12.965 1.00 0.00 LIPI ATOM 37 H3R POPE1 -11.533 -13.767 12.868 1.00 0.00 LIPI ATOM 38 H3S POPE1 -10.669 -15.218 13.434 1.00 0.00 LIPI ATOM 39 C24 POPE1 -11.678 -15.385 11.524 1.00 0.00 LIPI ATOM 40 H4R POPE1 -12.586 -14.837 11.192 1.00 0.00 LIPI ATOM 41 H4S POPE1 -10.819 -15.050 10.904 1.00 0.00 LIPI ATOM 42 C25 POPE1 -12.001 -16.882 11.443 1.00 0.00 LIPI ATOM 43 H5R POPE1 -11.079 -17.466 11.651 1.00 0.00 LIPI ATOM 44 H5S POPE1 -12.770 -17.181 12.187 1.00 0.00 LIPI ATOM 45 C26 POPE1 -12.435 -17.332 10.094 1.00 0.00 LIPI ATOM 46 H6R POPE1 -12.808 -18.375 10.172 1.00 0.00 LIPI ATOM 47 H6S POPE1 -13.247 -16.723 9.640 1.00 0.00 LIPI ATOM 48 C27 POPE1 -11.179 -17.198 9.148 1.00 0.00 LIPI ATOM
Re: [gmx-users] How to protonate a gmx trajectory?
Yun Shi wrote: Hi there, I am using GROMACS4.5.4 and the GROMOS 53A6 united-atom force field to do MD with my protein-ligand system. I was trying to add aliphatic hydrogens to the .gro and .trr or .xtc trajectory file with g_protonate, but the Fatal error was: Library file in current dir nor not found ffgmx2in defalt directories. Then re-name the directory in ../share/top/gmx2.ff to ffgmx2, and this time g_protonate seems to be able to find those .hdb files. But another error follows as: Reading frames from gro file 'Protein in water', 66743 atoms. Reading frame 0 time0.000 Opening force field file ffgmx2/aminoacids.hdb Opening force field file ffgmx2/atomtypes.atp Atomtype 1 Opening force field file ffgmx2/aminoacids.n.tdb Opening force field file ffgmx2/aminoacids.c.tdb Segmentation fault I searched for 'Segmentation fault', nothing relevant to g_protonate came up. A segmentation fault is a generic memory error that can be produced by any program. So I wonder if anyone could kindly help me out? Or is there an easy alternative way to protonate the trajectory file? The g_protonate program is currently nonfunctional. I have made a small fix in the release-4-5-patches branch, but the result is that the program can only handle .pdb files and nothing else. There is an outstanding issue that awaits a real resolution: http://redmine.gromacs.org/issues/589 In the meantime, I guess the only workaround is to generate .pdb files of each of your trajectory frames, then re-concatenate them as a new .xtc file. That would be somewhat tedious, but should work. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
[gmx-users] building a new molecule which does not exist in gmx data base
Dear Justin and other gmx-users, As per the journal article, Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies, PRODRG 2.5 server does not assign charges compatible with GROMOS force field. PRODRG 2.5, however, assigns the correct atom types and bonded parameters. I have to build 2,5-dihydroxybenzoic acid Starting from PRODRG 2.5 produced .itp and further rectification is a good idea? If yes, what should be strategy? And if PRODRG should not be my starting point at all, then how should I go about building the molecule/anion. Please guide, as I am not well versed with gromacs. Thanks, SN -- 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] building a new molecule which does not exist in gmx data base
shivangi nangia wrote: Dear Justin and other gmx-users, As per the journal article, Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies, PRODRG 2.5 server does not assign charges compatible with GROMOS force field. PRODRG 2.5, however, assigns the correct atom types and bonded parameters. I have to build 2,5-dihydroxybenzoic acid Starting from PRODRG 2.5 produced .itp and further rectification is a good idea? If yes, what should be strategy? As we state in the article, the topology provided by PRODRG is a reasonable template, but the charges and charge groups require modification. I've never seen a PRODRG topology that was correct at face value. That said, with adequate modification, the topology should be reasonable for use with Gromos96 43a1; other modifications (atom types, etc) may be necessary to make the topology compatible with other, more modern, Gromos96 parameter sets. And if PRODRG should not be my starting point at all, then how should I go about building the molecule/anion. Please guide, as I am not well versed with gromacs. For a molecule like yours, assigning charges and charge groups by analogy to existing functional groups should be a simple exercise. If this does not give a satisfactory result (based on validation methods discussed in the literature), then apply the charge calculations described in our article. Note that this task must be done with software external to Gromacs. If you are not very comfortable with these ideas, it is not wise to plow ahead blindly and hope for the best. Parameterization is an expert topic for a reason. It requires great care and a thorough understanding of the intrinsic features of the force field you wish to work with. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
[gmx-users] Directional Thermostat in GROMACS
Hi, I want to implement a directional thermostat in GROMACS. But I am not sure which files I will need to modify. Can anyone help me with this. I am using GROMACS 4.5.1. Thanks. Apoorv -- 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] Directional Thermostat in GROMACS
On 29/06/2011 5:49 AM, Apoorv Kalyankar wrote: Hi, I want to implement a directional thermostat in GROMACS. But I am not sure which files I will need to modify. Can anyone help me with this. I am using GROMACS 4.5.1. You'll have to look at how the existing T-coupling regimes work. src/mdlib/coupling.c for starters, but the best advice around is to get out a debugger and step through the whole code to learn the flow. Do yourself a favour and work from at least 4.5.4. Mark -- 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] R: gmx-users Digest, Vol 86, Issue 183
On 28/06/2011 8:09 PM, Anna Marabotti wrote: Dear Tsjerk, dear all, thank you very much for suggestion. One of the main reasons why I never used the rhombic dodecahedron box for my simulations is the fact that it is really hard to visualize the results with programs such as VMD or Pymol, and therefore I cannot check easily during the setting of my system if the work proceeds properly. Since I would like to redo my simulations following your suggestion, could you please give me some hints on how to proceed in order to visualize easily the system? In my experience, trjconv -pbc mol -ur compact is the way to achieve this. For example, now I created a dodecahedric box filled with water and ions. I tried to visualize it with VMD and I saw it as a rectangular box with the protein at one edge. I tried to use the command trjconv: trjconv -f prot_dod_box_neu.gro -s prot_dod_box_neu.tpr -o prot_dod_box_neu2.gro -pbc mol -ur compact and I obtained an error message stating: Fatal error: Index[84328] 84329 is larger than the number of atoms in the trajectory file (84328) The contents of the -f and -s files have to match meaningfully. Yours don't. I'm surprised this error message is as cryptic as it is. I'll make it less so. I don't find this error neither in the gmx-users list archive (indeed it's becoming harder and harder to search into this archive, given that each message is visualized 10 times, as I already noticed sometimes ago), nor in the Error section. The first .gro file is the one coming from genion, and the .tpr file is the one I used to neutralize the system, which is the .tpr file I should give to trjconv? For -pbc mol, trjconv needs to be told the definition of the molecules in the -f file. So you need to supply a .tpr that corresponds to it. Generating ions is a tricky case, because the output files do not match the input .tpr. Hence its scarcity in the archives. However, since you'll shortly be generating a .tpr file for the next stage, it's not a real problem for visualization. You see, if every time I try to use a box different from the standard cubic one I has to deal with such maybe trivial (for you) problems, but difficult and long to solve, I'm quite discouraged to use it! The only problem with the above is a small gap in understanding. I hope I've filled that now. This is also a kind request for Gromacs Web site managers: could you please add a section for this (recurrent, I suspect) problem of box visualization in the How-to section? it would be very useful for users, I think, and probably also for you (less trivial questions posted to the gmx-users list...) The web page is a wiki - anyone with useful contributions is welcome to make them, but registering an account for editing does require registration. People who've experienced and solved a problem are often well placed to document management strategies :-) Others will come along and flesh out details, etc. Mark -- 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] trjorder and index
Hi, I am trying to use trjorder command to generate a sorted trajectory where all the water molecules are certain distance away. I can use the trjorder command to generate the sorted trajectory where all waters are sorted based on distance but I am looking for method for creating a index file which will have only those water molecules which are ,say 0.4 nm away from protein. So far, I could not find any way in trjorder which can give me an index file containing the water molecules certain distance away. -nshell option in trjorder only gives the number of water molecules within a distance but does not specify their indices. Also, since the water molecules are always fluctuating, the number of water within a certain distance and their indexing will change all the time. So, I was wondering whether you can suggest a way where I can create an index file from the sorted trajectory so as to have only those waters which are certain distance away. I mean : is there any way in make_ndx tool , where one can do it using certain keywords. Any help will be really appreciated. Sanku-- 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] trjorder and index
Sanku M wrote: Hi, I am trying to use trjorder command to generate a sorted trajectory where all the water molecules are certain distance away. I can use the trjorder command to generate the sorted trajectory where all waters are sorted based on distance but I am looking for method for creating a index file which will have only those water molecules which are ,say 0.4 nm away from protein. So far, I could not find any way in trjorder which can give me an index file containing the water molecules certain distance away. -nshell option in trjorder only gives the number of water molecules within a distance but does not specify their indices. Also, since the water molecules are always fluctuating, the number of water within a certain distance and their indexing will change all the time. So, I was wondering whether you can suggest a way where I can create an index file from the sorted trajectory so as to have only those waters which are certain distance away. I mean : is there any way in make_ndx tool , where one can do it using certain keywords. Dynamic selections can be created with g_select, not make_ndx. The g_select output will be an index group for each frame, which (to my knowledge) cannot be automatically used by any Gromacs tool yet, but you can certainly select frames that correspond to these groups to write out a given frame. The other problem is that you'll potentially have different numbers of atoms in each frame, making assembling a single trajectory impossible. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
[gmx-users] converting psf file to gromacs .itp file
Hi, Is there any way to convert NAMD generated psf file to GROMACS .itp file as I have generated the parameters for my compound using NAMD.. -- Bharat -- 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] converting psf file to gromacs .itp file
bharat gupta wrote: Hi, Is there any way to convert NAMD generated psf file to GROMACS .itp file as I have generated the parameters for my compound using NAMD.. Both are just text files; use your favorite scripting language to convert between the two. There is a program called top2psf.pl that is available from the User Contributions page on the Gromacs site that does the opposite (.itp to .psf) that you may be able to reverse engineer for your purpose. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
