Re: [gmx-users] query about protein-ligand complex
Hi Sangeeta, Also check whether you have isolated water molecules in your system (notably the one starting at atom id 13339). If so, that may be a cause of crash and it would be better just to delete the water molecule. Best, Tsjerk On 7/3/06, Mark Abraham [EMAIL PROTECTED] wrote: sangeeta wrote: I could not mail you as our net was down, you asked me Is your system properly minimized? My question is how can I understand whether my system is properly minimised? Look at the structure before you minimize it, and look at the structure after you minimize it. See what has changed and use some chemical judgement. If you're uncertain of yourself, experiment with some smaller systems before using a system as large as yours. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] query about protein-ligand complex
I could not mail you as our net was down, you asked me Is your system properly minimized? My question is how can I understand whether my system is properly minimised? the run is still going on, I can realize that something is going wrong. But I can not detect it.The log file is giving the error that the system is not properly minimised.I am giving you the messege, 2127 2131 176.6 223178260480. 3921810030592. 0.1330 2128 2129 176.6 69075034112. 1233987043328. 0.1000 2128 2130 176.6 69075394560. 1233986912256. 0.1000 2131 2132 176.5 69056528384. 1233902108672. 0.1000 2131 2133 176.5 69054996480. 1233896734720. 0.1000 Constraint error in algorithm Lincs at step 9 t = 0.018 ps: Water molecule starting at atom 13339 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates Large VCM(group rest): -168597.92188, 112023.07031, -175543.56250, ekin-cm: 3.95206e+15 will you please give me some suggestion , so that I can run the system from the beginning? regards Sangeeta On Fri, 30 Jun 2006 14:50:44 +0200, Erik Marklund wrote On Fri, 2006-06-30 at 17:52 +0530, sangeeta wrote: Dear all, I am trying to run the dynamics of protein-ligand complex following the tutorial GROMACS Tutorial for Drug_Enzyme Complex version 3.3.1 . I am running position restricted dynamics of the 91az8.pdb protein as mentioned in the tutorial trp.pdb drg.pdb)in a Linux server machine, I can not understand why it is taking such a long time, the machine is not busy with any other jobs.I ran it before I stopped the run at 1200 min, now it is going for about 215 min, step6.pdb, step7.pdb etc files are being formed, I can not undersyand whether I am doing any wrong step, why it is taking such a long time , I don't know , please help. stepX.pdb files are generated when things go wrong, for example when forces or other quantities becomes NaN or Inf. The log files should give some clues about what is happening to your system.Is your system properly minimized? Please provide some more information, otherwise it's difficult to help you. /Erik Marklund regards sangeeta Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Erik Marklund, PhD Student, Molecular Biopcysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4537 fax: 46 18 511 755 [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] query about protein-ligand complex
Dear all, I am trying to run the dynamics of protein-ligand complex following the tutorial GROMACS Tutorial for Drug_Enzyme Complex version 3.3.1 . I am running position restricted dynamics of the 91az8.pdb protein as mentioned in the tutorial trp.pdb drg.pdb)in a Linux server machine, I can not understand why it is taking such a long time, the machine is not busy with any other jobs.I ran it before I stopped the run at 1200 min, now it is going for about 215 min, step6.pdb, step7.pdb etc files are being formed, I can not undersyand whether I am doing any wrong step, why it is taking such a long time , I don't know , please help. regards sangeeta Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] query about protein-ligand complex
On Fri, 2006-06-30 at 17:52 +0530, sangeeta wrote: Dear all, I am trying to run the dynamics of protein-ligand complex following the tutorial GROMACS Tutorial for Drug_Enzyme Complex version 3.3.1 . I am running position restricted dynamics of the 91az8.pdb protein as mentioned in the tutorial trp.pdb drg.pdb)in a Linux server machine, I can not understand why it is taking such a long time, the machine is not busy with any other jobs.I ran it before I stopped the run at 1200 min, now it is going for about 215 min, step6.pdb, step7.pdb etc files are being formed, I can not undersyand whether I am doing any wrong step, why it is taking such a long time , I don't know , please help. stepX.pdb files are generated when things go wrong, for example when forces or other quantities becomes NaN or Inf. The log files should give some clues about what is happening to your system. Is your system properly minimized? Please provide some more information, otherwise it's difficult to help you. /Erik Marklund regards sangeeta Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Erik Marklund, PhD Student, Molecular Biopcysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4537 fax: 46 18 511 755 [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
