[gmx-users] checking gen_seed
Hi all, I've accidentally deleted my mdp and .tpr file.. :( Is there a way I could check the gen_seed of my simulation from the .tpr or the output of my simulation as I need the info to simulate the same system at another temerature? Thanks. Joyce -- 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] checking gen_seed
Alright, thx Mark. From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, March 22, 2011 15:44:51 Subject: Re: [gmx-users] checking gen_seed On 22/03/2011 6:28 PM, Kwee Hong wrote: Hi all, I've accidentally deleted my mdp and .tpr file.. :( Is there a way I could check the gen_seed of my simulation from the .tpr or the output of my simulation as I need the info to simulate the same system at another temerature? I don't think gen_seed is saved in the .tpr, but you can see with gmxdump. At a different temperature it generates different velocities anyway, so I don't think there is value in controlling this variable. More importantly, if you're simulating long enough to approach convergence, the value of gen_seed doesn't matter because the simulation has converged. If you're not simulating that long, then it also doesn't matter, in that your results won't be worth much even if you used the same gen_seed at the same temperature... 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] only one model is displayed
Hi, I've used g_confrms from gromacs-4.5.1 to compare two structures with the following command line - g_confrms -f1 1OMB.pdb -f2 md.gro -o fit.pdb fit.pdb is supposed to be the output file which would show the 2 structures superimposed on each other. But when I visualised it with vmd. I can only see one structure. Any idea what's going on? I hereby attached part of the generated fit.pdb. All suggestions are welcomed. Regards, Joyce -- 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: only one model is displayed
sorry, forgot to attached the file... From: Kwee Hong jestan1...@yahoo.com To: gmx-users gmx-users@gromacs.org Sent: Friday, February 11, 2011 23:38:55 Subject: only one model is displayed Hi, I've used g_confrms from gromacs-4.5.1 to compare two structures with the following command line - g_confrms -f1 1OMB.pdb -f2 md.gro -o fit.pdb fit.pdb is supposed to be the output file which would show the 2 structures superimposed on each other. But when I visualised it with vmd. I can only see one structure. Any idea what's going on? I hereby attached part of the generated fit.pdb. All suggestions are welcomed. Regards, Joyce fit.pdb Description: Binary data -- 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] doubts on g_confrms output
Hi Tsjerk, Thanks for the help. I got it. But do you have any idea how to solve this in vmd? Regards, Joyce From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, January 22, 2011 15:53:22 Subject: Re: [gmx-users] doubts on g_confrms output Hi Joyce, In pymol use 'set all_states' Cheers, Tsjerk On Jan 22, 2011 8:30 AM, Kwee Hong jestan1...@yahoo.com wrote: Hi, I was trying to do some analysis following John's GROMACS tutorial for solvation study of spider toxin peptide. I'm using GROMACS-4.5.3 and my command line for g_confrms is g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb The program calculated the RMSD sucessfully and fit_wet.pdb was generated. Yet, when i tried to visualise fit_wet.pdb using VMD, the structure is obviously in a mess. And when I tried it out with pymol, I can only visualised one model. Model 2 did not appear. I wonder would it be the pdb format generated by g_confrms is not the standard pdb format and had caused VMD and final failed to read them? Herein, I attached part of the pdb file generated by fit_wet.pdb. Any insight is welcomed. Thanks, Joyce -- 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 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] doubts on g_confrms output
Hi Mark, I tried but with this error: Fatal error: Number of atoms in pdb frame 0 is 331 instead of 491 Joyce From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, February 12, 2011 0:01:39 Subject: Re: [gmx-users] doubts on g_confrms output On 12/02/2011 2:55 AM, Kwee Hong wrote: Hi Tsjerk, Thanks for the help. I got it. But do you have any idea how to solve this in vmd? Use trjconv -sep on the .pdb file to split it. Mark Regards, Joyce From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, January 22, 2011 15:53:22 Subject: Re: [gmx-users] doubts on g_confrms output Hi Joyce, In pymol use 'set all_states' Cheers, Tsjerk On Jan 22, 2011 8:30 AM, Kwee Hong jestan1...@yahoo.com wrote: Hi, I was trying to do some analysis following John's GROMACS tutorial for solvation study of spider toxin peptide. I'm using GROMACS-4.5.3 and my command line for g_confrms is g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb The program calculated the RMSD sucessfully and fit_wet.pdb was generated. Yet, when i tried to visualise fit_wet.pdb using VMD, the structure is obviously in a mess. And when I tried it out with pymol, I can only visualised one model. Model 2 did not appear. I wonder would it be the pdb format generated by g_confrms is not the standard pdb format and had caused VMD and final failed to read them? Herein, I attached part of the pdb file generated by fit_wet.pdb. Any insight is welcomed. Thanks, Joyce -- 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 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] invacuo simulation
Hi In John's GROMACS tutorial for solvation study of spider toxin peptide,I keep on getting an error message at the production stage: Step 12111 Warning: Pressure scaling more than 1%. Step 12121 Warning: Pressure scaling more than 1%. Step 12131 Warning: Pressure scaling more than 1%. --- Program mdrun, VERSION 4.5.1 Source code file: ns.c, line: 2544 Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I've tried a few approaches after reading the mailing list yet I'm still getting the same error message. The command lined I used in this simulation is as follow: pdb2gmx -ignh -ff gtomos43a1 -f 1OMB.pdb -o fws.pdb -p fws.top -water spce editconf -bt cubic -f fws.pdb -o fws.pdb -d 1.0 grompp -f em.mdp -c fws.pdb -p fws.top -o em.tpr -maxwarn 5 mdrun -v -deffnm em grompp -f md.mdp -c em.gro -p fws.top -o md.tpr -maxwarn 3 mdrun -v -deffnm md After getting the error above round step 2300, I increased the tau_p from 0.5 to 1.0. Yet I got the same error message at step 5400 though the warning on pressure scaling more than 1% was gone. Therefore, I inceased the -d option in editconf to 1.5. But once again, I got the same error message at step 7300 (no warning on pressure scaling). So once again, I increased the -d option in editconf to 2.5. And I still got the same error message at step 11300. I'm now real lost in solving this.. I hereby attach my full.mdp file, hopefully to get some insight here. Any suggestions are appreciated. Thanks. Regards, Joyce md.mdp Description: Binary data -- 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] invacuo simulation
From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, January 28, 2011 17:51:41 Subject: Re: [gmx-users] invacuo simulation On 28/01/2011 8:45 PM, Kwee Hong wrote: Hi In John's GROMACS tutorial for solvation study of spider toxin peptide,I keep on getting an error message at the production stage: Step 12111 Warning: Pressure scaling more than 1%. Step 12121 Warning: Pressure scaling more than 1%. Step 12131 Warning: Pressure scaling more than 1%. --- Program mdrun, VERSION 4.5.1 Source code file: ns.c, line: 2544 Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I've tried a few approaches after reading the mailing list yet I'm still getting the same error message. The command lined I used in this simulation is as follow: pdb2gmx -ignh -ff gtomos43a1 -f 1OMB.pdb -o fws.pdb -p fws.top -water spce Typo there. Sorry for the typo editconf -bt cubic -f fws.pdb -o fws.pdb -d 1.0 grompp -f em.mdp -c fws.pdb -p fws.top -o em.tpr -maxwarn 5 mdrun -v -deffnm em grompp -f md.mdp -c em.gro -p fws.top -o md.tpr -maxwarn 3 mdrun -v -deffnm md Look at those warnings. Unless you know what they are and why ignoring them is OK, don't use -maxwarn. There is actually no warning but note: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing I think this is not significant since I'm running the simulation on single workstation. After getting the error above round step 2300, I increased the tau_p from 0.5 to 1.0. Yet I got the same error message at step 5400 though the warning on pressure scaling more than 1% was gone. Therefore, I inceased the -d option in editconf to 1.5. But once again, I got the same error message at step 7300 (no warning on pressure scaling). So once again, I increased the -d option in editconf to 2.5. And I still got the same error message at step 11300. I'm now real lost in solving this.. I hereby attach my full.mdp file, hopefully to get some insight here. Any suggestions are appreciated. .mdp file looks OK. Mark Thanks. Regards, Joyce -- 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] doubts on running em in vacuo
Hi In John's GROMACS tutorial for solvation study of spider toxin peptide, he has included a suggested em.mdp files to set up an in vacuo minimization. But I had some noted while conducting the grompp before em. Analysing residue names: There are:35Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 990.00 Largest charge group radii for Van der Waals: 0.238, 0.238 nm Largest charge group radii for Coulomb: 0.238, 0.238 nm NOTE 2 [file em_steep.mdp]: The sum of the two largest charge group radii (0.476006) is larger than rlist (1.40) - rvdw (1.00) NOTE 3 [file em_steep.mdp]: The sum of the two largest charge group radii (0.476006) is larger than rlist (1.40) - rcoulomb (1.00) This run will generate roughly 0 Mb of data There were 3 notes Back Off! I just backed up em.tpr to ./#em.tpr.1# gcq#243: Uh-oh Right Again (Laurie Anderson) I've read through some of the posts in the mailing list and realised that doing some adjustment on the cut-off would solve this. Yet I'm not sure how to justify the adjustment. Option A: Increase my rlist to 1.5 leaving the rest cut-off at 1.0? And set my rcoulomb_switch and rvdw_swithch at 0.8? Option B: Increase my rlist to 1.6 while leaving the rest cut-off at 1.2 and set my rcoulomb_switch and rvdw_swithch at 1.0? I'm using GROMACS-4.5.3. And I attach mt em_steep.mdp file i this email. Suggestions are all welcomed. Thanks, Joyce em_steep.mdp Description: Binary data -- 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] doubts on g_confrms output
Hi, I was trying to do some analysis following John's GROMACS tutorial for solvation study of spider toxin peptide. I'm using GROMACS-4.5.3 and my command line for g_confrms is g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb The program calculated the RMSD sucessfully and fit_wet.pdb was generated. Yet, when i tried to visualise fit_wet.pdb using VMD, the structure is obviously in a mess. And when I tried it out with pymol, I can only visualised one model. Model 2 did not appear. I wonder would it be the pdb format generated by g_confrms is not the standard pdb format and had caused VMD and final failed to read them? Herein, I attached part of the pdb file generated by fit_wet.pdb. Any insight is welcomed. Thanks, Joyce fit_wet.pdb Description: Binary data -- 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] pdb2gmx: segmentation fault
Hi Tsjerk, Ya, it happened with other ff, too. My command line is pdb2gmx -ignh -f Sur.pdb i've browsed through the pdb file and it looks ok... joyce From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, January 13, 2011 15:31:35 Subject: Re: [gmx-users] pdb2gmx: segmentation fault Hi Joyce, Can you post the command line? Does it also happen with other force fields? Is there something notable about the pdb file? Cheers, Tsjerk On Jan 13, 2011 7:48 AM, Kwee Hong jestan1...@yahoo.com wrote: Hi Mark, I tried v 4.0.7 and 4.5.1. Both experiencing the same situation. The file is actually saved as pdb file from autodock output using pymol. Joyce From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, January 13, 2011 13:43:47 Subject: Re: [gmx-users] pdb2gmx: segmentation fault On 01/13/11, Kwee Hong jestan1...@yahoo.com wrote: Hi,I was trying to generate topolo... -- 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 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: pdb2gmx: segmentation fault
Hi all, I've uploaded my pdb file at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Maybe someone can help me to look into it and see does it has any error. Thanks, Joyce From: Kwee Hong jestan1...@yahoo.com To: gmx-users gmx-users@gromacs.org Sent: Thursday, January 13, 2011 12:21:55 Subject: pdb2gmx: segmentation fault Hi, I was trying to generate topology file of my pdb using pdb2gmx. Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges 4 Opening library file /usr/share/gromacs/top/ffG53a6.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading complex_SurA.pdb... Read 3163 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 409 residues with 3163 atoms chain #res #atoms 1 'B' 409 3163 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/share/gromacs/top/ffG53a6.atp Atomtype 1 Reading residue database... (ffG53a6) Opening library file /usr/share/gromacs/top/ffG53a6.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening library file /usr/share/gromacs/top/ffG53a6.hdb Opening library file /usr/share/gromacs/top/ffG53a6-n.tdb Opening library file /usr/share/gromacs/top/ffG53a6-c.tdb Back Off! I just backed up topol_SurA.top to ./#topol_SurA.top.1# Processing chain 1 'B' (3163 atoms, 409 residues) There are 629 donors and 614 acceptors Segmentation fault Yet I encountered segmentation fault which I don't understand why this happen. All suggestion are welcomed? Thanks. Joyce -- 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] Re: pdb2gmx: segmentation fault
Sorry, this should be correct link to download the file. http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb Joyce From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, January 14, 2011 11:29:45 Subject: Re: [gmx-users] Re: pdb2gmx: segmentation fault On 01/14/11, Kwee Hong jestan1...@yahoo.com wrote: Hi all, I've uploaded my pdb file at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Maybe someone can help me to look into it and see does it has any error. That link does not work. 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] Re: pdb2gmx: segmentation fault
Sorry. Sorry. This would be the working one. I've tested it outside my uni domain. http://www.birg1.fbb.utm.my/joyce/protein_dock.pdb joyce From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, January 14, 2011 11:57:01 Subject: Re: [gmx-users] Re: pdb2gmx: segmentation fault Kwee Hong wrote: Sorry, this should be correct link to download the file. http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb This link also does not work. -Justin http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Joyce *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, January 14, 2011 11:29:45 *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault On 01/14/11, *Kwee Hong * jestan1...@yahoo.com wrote: Hi all, I've uploaded my pdb file at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Maybe someone can help me to look into it and see does it has any error. That link does not work. Mark -- 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 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] Re: pdb2gmx: segmentation fault
It works. Thanks a lot From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Friday, January 14, 2011 12:18:45 Subject: Re: [gmx-users] Re: pdb2gmx: segmentation fault Kwee Hong wrote: Sorry. Sorry. This would be the working one. I've tested it outside my uni domain. http://www.birg1.fbb.utm.my/joyce/protein_dock.pdb Remove the www and it works for me. Your .pdb file has several problems: 1. Loads of blank space at the end. 2. All lines are misformatted, with all columns after the chain identifier shifted by one space. In vi, use :1,$s/ B / B/g to fix it. This alleviates the seg fault. 3. Asn106 has its N atom labeled as residue 105. Fixing all of the above resulted in a usable topology with Gromacs 4.5.3. -Justin http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb joyce *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, January 14, 2011 11:57:01 *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault Kwee Hong wrote: Sorry, this should be correct link to download the file. http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb This link also does not work. -Justin http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Joyce *From:* Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Friday, January 14, 2011 11:29:45 *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault On 01/14/11, *Kwee Hong * jestan1...@yahoo.com mailto:jestan1...@yahoo.com wrote: Hi all, I've uploaded my pdb file at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Maybe someone can help me to look into it and see does it has any error. That link does not work. Mark -- 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 mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 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] Re: pdb2gmx: segmentation fault
But Justin got it... From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, January 14, 2011 12:18:49 Subject: Re: [gmx-users] Re: pdb2gmx: segmentation fault On 01/14/11, Kwee Hong jestan1...@yahoo.com wrote: Sorry. Sorry. This would be the working one. I've tested it outside my uni domain. http://www.birg1.fbb.utm.my/joyce/protein_dock.pdb Still dead. Mark joyce From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, January 14, 2011 11:57:01 Subject: Re: [gmx-users] Re: pdb2gmx: segmentation fault Kwee Hong wrote: Sorry, this should be correct link to download the file. http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb This link also does not work. -Justin http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Joyce *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, January 14, 2011 11:29:45 *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault On 01/14/11, *Kwee Hong * jestan1...@yahoo.com wrote: Hi all, I've uploaded my pdb file at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Maybe someone can help me to look into it and see does it has any error. That link does not work. Mark -- 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 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] pdb2gmx: segmentation fault
Hi, I was trying to generate topology file of my pdb using pdb2gmx. Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges 4 Opening library file /usr/share/gromacs/top/ffG53a6.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading complex_SurA.pdb... Read 3163 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 409 residues with 3163 atoms chain #res #atoms 1 'B' 409 3163 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/share/gromacs/top/ffG53a6.atp Atomtype 1 Reading residue database... (ffG53a6) Opening library file /usr/share/gromacs/top/ffG53a6.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening library file /usr/share/gromacs/top/ffG53a6.hdb Opening library file /usr/share/gromacs/top/ffG53a6-n.tdb Opening library file /usr/share/gromacs/top/ffG53a6-c.tdb Back Off! I just backed up topol_SurA.top to ./#topol_SurA.top.1# Processing chain 1 'B' (3163 atoms, 409 residues) There are 629 donors and 614 acceptors Segmentation fault Yet I encountered segmentation fault which I don't understand why this happen. All suggestion are welcomed? Thanks. Joyce -- 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] pdb2gmx: segmentation fault
Hi Mark, I tried v 4.0.7 and 4.5.1. Both experiencing the same situation. The file is actually saved as pdb file from autodock output using pymol. Joyce From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, January 13, 2011 13:43:47 Subject: Re: [gmx-users] pdb2gmx: segmentation fault On 01/13/11, Kwee Hong jestan1...@yahoo.com wrote: Hi, I was trying to generate topology file of my pdb using pdb2gmx. Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges 4 Opening library file /usr/share/gromacs/top/ffG53a6.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading complex_SurA.pdb... Read 3163 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 409 residues with 3163 atoms chain #res #atoms 1 'B' 409 3163 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/share/gromacs/top/ffG53a6.atp Atomtype 1 Reading residue database... (ffG53a6) Opening library file /usr/share/gromacs/top/ffG53a6.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening library file /usr/share/gromacs/top/ffG53a6.hdb Opening library file /usr/share/gromacs/top/ffG53a6-n.tdb Opening library file /usr/share/gromacs/top/ffG53a6-c.tdb Back Off! I just backed up topol_SurA.top to ./#topol_SurA.top.1# Processing chain 1 'B' (3163 atoms, 409 residues) There are 629 donors and 614 acceptors Segmentation fault Yet I encountered segmentation fault which I don't understand why this happen. All suggestion are welcomed? Please remember to announce your GROMACS version when discussing problems, and to try the latest one. 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] top2psf.pl is generating some bonds to atoms with index 0.
Alright.. I actually simulated my protein for 5ns. Then I loaded the trajectory file and .gro file in vmd. Then, I extracted one of the frame and write it into pdb format, When I open it with vmd, one of the atom from a residue is connected to another atom in another residue. Things like this happens as VMD uses a distance-based bond determination heuristic. Therefore, I would need a structure file which specifies the bonds for my structure so that VMD doesn't have to guess. So how can I generate the structure file I needed? Thanks. Regards, Joyce From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Wednesday, October 20, 2010 2:25:26 Subject: Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0. Kwee Hong wrote: I executed the script at the therminal by typing perl top2psf.pl -i topol.top -o zz.psf Here, I attached my input file. Your topology does not correspond to a MARTINI coarse-grained topology. As such, probably a bunch of the pattern matching is getting incorrect information. You cannot use top2psf.pl with this type of topology. It was created for a very specific purpose and requires that format, nothing else. -Justin *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, October 20, 2010 2:14:34 *Subject:* Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0. Kwee Hong wrote: Hi, I've got a top2psf.pl script from the web and used it to generate a psf file. Yet it generated some bonds to atoms with index 0 which should not occur. It causes VMD cannot load it and had a segmentation fault. vmd Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf ERROR) Error reading bond information. Segmentation fault I wonder am I getting the right top2psf.pl. Or is there any place I can get the latest stable version of that script? There is only one version. Zeros are only printed if something goes wrong, i.e. you have provided the wrong input or something else has failed. Based solely on the information you've provided I cannot diagnose what has gone wrong. -Justin Here, I attached the perl script I used. Thanks. Regards, Joyce -- 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 mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 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] top2psf.pl is generating some bonds to atoms with index 0.
Hi, I've got a top2psf.pl script from the web and used it to generate a psf file. Yet it generated some bonds to atoms with index 0 which should not occur. It causes VMD cannot load it and had a segmentation fault. vmd Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf ERROR) Error reading bond information. Segmentation fault I wonder am I getting the right top2psf.pl. Or is there any place I can get the latest stable version of that script? Here, I attached the perl script I used. Thanks. Regards, Joyce top2psf.pl Description: Binary data -- 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] problem while simulating metal ions
Hi. I'm trying to subject a metalloprotein bound to cadmium to a molecular dynamics. I've defined the cadmium ion in the atom type parameter file (ffGa56a6.atp) and residue database (ffG53a6.rtp). And the bond length and bond angle between the cadmium and sulphur of the metalloprotein had been define in the force field file, too (ffG53a6abon.itp). As special bond is expected to be formed between the sulphur of cysteine and the cadmium ions, I've added the relevant information into specbond.dat. But when I run the pdb2gmx, there is no entries in the [ bonds ] and [ angles ] for those bond length and bond angle. And of course, as there is no entries in those parameter, there was no cadmium-thiolate bond observed when I visualised the structure using pymol. So, does that mean that I would need to add them on manually? To proceed with my simulation, I added the values in [ bonds ] and [ angles ] manually. And as I do not have the relevant dihedral angle value from the literature, I've deleted those entries in my topology file and continue to prepare and subject the protein to energy minimization. During EM, the potential energy of the system started to remain constant at step 124 and eventually steepest descents converged to machine precision in 128 steps with the maximum force is on atom 279 which would be one of the cadmium ions in the system. When I visualised the system, one water molecule was found to attached with atom 279, so I deleted that water molecule and subject the system to em again. Yet the same thing occur after running for 49 steps. What had gone wrong with my system? Is that cadmium molecule had been running too far until it has gone out of the protein as water molecule are not suppose to come into the protein. Any suggestion is welcomed. Thanks in advance. Regards, Joyce -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 on forming bonds
Hi. I'm trying to subject a metalloprotein bound to cadmium to a molecular dynamics. I've defined the cadmium ion in the atom type parameter file (ffGa56a6.atp) and residue database (ffG53a6.rtp). And the bond length and bond angle between the cadmium and sulphur of the metalloprotein had been define in the force field file, too (ffG53a6abon.itp). As special bond is expected to be formed between the sulphur of cysteine and the cadmium ions, I've added the relevant information into specbond.dat. But when I run the pdb2gmx, there is no entries in the [ bonds ] and [ angles ] for those bond length and bond angle. I've attached a sample of the topology generated by pdb2gmx in the attachment. Please kindly refer to it. And of course, as there is no entries in those parameter, there was no cadmium-thiolate bond observed when I visualised the structure using pymol. So, does that mean that I would need to add them on manually? To proceed with my simulation, I added the values in [ bonds ] and [ angles ] manually. And as I do not have the relevant dihedral angle value from the literature, I've deleted those entries in my topology file and continue to prepare and subject the protein to energy minimization. During EM, the potential energy of the system started to remain constant at step 124 and eventually steepest descents converged to machine precision in 128 steps with the maximum force is on atom 279 which would be one of the cadmium ions in the system. When I visualised the system, one water molecule was found to attached with atom 279, so I deleted that water molecule and subject the system to em again. Yet the same thing occur after running for 49 steps. What had gone wrong with my system? Is that cadmium molecule had been running too far until it has gone out of the protein as water molecule are not suppose to come into the protein. Any suggestion is welcomed. Thanks in advance. Regards, Joyce topol_sample Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] Downloading DSSP onto iMAC
Hi. I'm in the midst of downloading DSSP onto my iMAC. But I'm having some error here: rsync: failed to connect to rsync.cmbi.ru.nl: Connection refused (61) rsync error: error in socket IO (code 10) at /SourceCache/rsync/rsync-35.2/rsync/clientserver.c(105) [receiver=2.6.9] I suppose it is caused by the syntax (rsync) I'm using as I'm trying to download onto iMAC and not linux. Can someone tell me the correct syntax to do so? Thanks. Regards, Joyce ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
Hi. When I was trying to do the test run for my installed gromacs, I got message below return to me even though i've source GMXRC (source /usr/local/gromacs/bin/GMXRC). Can some one tell me why? Thanks. bcsb09s-imac52:bin bcsb09$ ./gmxtest.pl all 102 out of 102 simple tests FAILED sh: grompp.out: Permission denied No topol.tpr file in bin. grompp failed FAILED. Check files in bin sh: grompp.out: Permission denied No topol.tpr file in include. grompp failed FAILED. Check files in include sh: grompp.out: Permission denied No topol.tpr file in lib. grompp failed FAILED. Check files in lib sh: grompp.out: Permission denied No topol.tpr file in share. grompp failed FAILED. Check files in share 4 out of 4 complex tests FAILED sh: grompp.out: Permission denied No topol.tpr file in OpenSourceLicenses. grompp failed FAILED. Check files in OpenSourceLicenses sh: grompp.out: Permission denied No topol.tpr file in OpenSourceVersions. grompp failed FAILED. Check files in OpenSourceVersions sh: grompp.out: Permission denied No topol.tpr file in bin. grompp failed FAILED. Check files in bin sh: grompp.out: Permission denied No topol.tpr file in gromacs. grompp failed FAILED. Check files in gromacs sh: grompp.out: Permission denied No topol.tpr file in i386-mingw32-3.4.5. grompp failed FAILED. Check files in i386-mingw32-3.4.5 sh: grompp.out: Permission denied No topol.tpr file in include. grompp failed FAILED. Check files in include sh: grompp.out: Permission denied No topol.tpr file in info. grompp failed FAILED. Check files in info sh: grompp.out: Permission denied No topol.tpr file in lib. grompp failed FAILED. Check files in lib sh: grompp.out: Permission denied No topol.tpr file in share. grompp failed FAILED. Check files in share 9 out of 9 kernel tests FAILED Opening pdb2gmx.log for writing at ./gmxtest.pl line 300. Regards.. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] cannot generate .top file
Hi. Thanks for your enlightenment. Now, I'm able to run pdb2gmx with the output files produced. I just added 'sudo' before ./pdb2gmx and it allows me to write in the directory. But unfortunately, this step seem does not work for ./gmxtest.pl. I'm having the same output even after i had added 'sudo' in front of it. Joyce On Fri, Oct 24, 2008 at 8:52 PM, Mark Abraham [EMAIL PROTECTED]wrote: Kwee Hong wrote: Hi. I seem having some problem in running ./pdb2gmx. Here is the output file. Can you help me in giving me some idea to deal with this? bcsb09s-imac52:bin bcsb09$ pdb2gmx -f 1aml.pdb -p 1aml.top -o 1aml.gro snip --- Program pdb2gmx, VERSION 3.3.3 Source code file: futil.c, line: 313 File input/output error: 1aml.top --- This means it can't write 1aml.top, which likely means you don't have write permission to the directory in which pdb2gmx resides. This is a Good Thing. You should do daily work in a suitable subdirectory of (say) your home directory, and adjust your environment variables to give you ready access to GROMACS stuff by using source /path/to/GMXRC using the path in which you installed the GROMACS binaries. I guess this is your attempted working directory above. I seem to be having problem in running the test tun as well. Below is its output: bcsb09s-imac52:bin bcsb09$ ./gmxtest.pl Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | complex | kernel | pdb2gmx | all ] or: ./gmxtest.pl clean | refclean | dist Again this won't work in a directory in which you don't have write permissions. The above message tells you that an empty command line isn't acceptable to gmxtest.pl. *Technically* it ought to be acceptable per the usage line, since square brackets denote optional things and |-symbols denote a series of mutually-exclusive possibilities. I think the brackets should be missing around simple | complex | kernel | pdb2gmx | all. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] cannot generate .top file
Oo.. I'm so sorry for I'm not aware of this. But I'm really new to linux environment and don't really have a good mastering skill on the commandline that it works with. As you said that I'm not given the permission to write in that directory, sudo was the only thing that I can think of out from my knowledge. I don't really know how to do my work at the subdirectory of my hoe directory. And does the meaning of adjust your environment variables to give you ready access to GROMACS stuff by using source /path/to/GMXRC using the path in which you installed the GROMACS binaries requires me to make some changes in the source code or just by typing source /path/to/GMXRC at the terminal would have open the access for me in the directory? I'm sorry for my ignorance... I think I would better get some books on linux environment and read on it first. Joyce On Wed, Oct 29, 2008 at 12:11 PM, Mark Abraham [EMAIL PROTECTED]wrote: Kwee Hong wrote: Hi. Thanks for your enlightenment. Now, I'm able to run pdb2gmx with the output files produced. I just added 'sudo' before ./pdb2gmx and it allows me to write in the directory. But unfortunately, this step seem does not work for ./gmxtest.pl. I'm having the same output even after i had added 'sudo' in front of it. If you do this kind of thing, your machine is a ticking time bomb. I gave you good advice last time. I'm not going to give you more :-) 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] cannot generate .top file
Hi. I seem having some problem in running ./pdb2gmx. Here is the output file. Can you help me in giving me some idea to deal with this? bcsb09s-imac52:bin bcsb09$ pdb2gmx -f 1aml.pdb -p 1aml.top -o 1aml.gro :-) G R O M A C S (-: Getting the Right Output Means no Artefacts in Calculating Stuff :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description -f 1aml.pdb InputGeneric structure: gro g96 pdb tpr tpb tpa xml -o 1aml.gro Output Generic structure: gro g96 pdb xml -p 1aml.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Generic structure: gro g96 pdb xml Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]merge bool no Merge chains into one molecule definition -ff string select Force field, interactive by default. Use -h for information. -water enum spc Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p or f3c -[no]inter bool no Set the next 6 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool no Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]arg bool no Interactive Arganine selection, iso charged -[no]asp bool no Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged -[no]gln bool no Interactive Glutamine selection, iso neutral -[no]his bool no Interactive Histidine selection, iso checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -distreal 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine -[no]ignhbool no Ignore hydrogen atoms that are in the pdb file -[no]missing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000Force constant for position restraints -vsite enum noneConvert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: Encad all-atom force field, using scaled-down vacuum charges 8: Encad all-atom force field, using full solvent charges 2 Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Reading 1aml.pdb... Read 'AMYLOID A4', 598 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 40 residues with 598 atoms chain #res #atoms 1 ' '40598 All occupancies are one Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.atp Atomtype 50 Reading residue database... (ffG43a2) Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.rtp Residue 96 Sorting it all out... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.hdb Opening library file
[gmx-users] Installation on iMAC
Hi. I'm very new to iMAC as I've just started to use it for about one month. I would like to install GROMACS on it but i seem can't find any step-to-step installation instruction. All those that I found was seem to be instruction for linux. Can you give me some idea on how to get the installation instruction? Thank you very much. Best regards, Joyssstan ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
