[gmx-users] (no subject)
Dear Gromacs users, I want to study the thermostability of a protein using MD simulations. I will be thankful if someone could guide me to do this job. Regards Harpreet Singh -- 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] regarding grompp using constraints
Hi I am running grompp command for energy minimization (using steep). Force field used is g34a1 operating system is Linux The input file attached herewith is only 5 amino acids long test file (The file is attached herewith). Using other constraints the program is running very fast but if I am using constraints = h-angles or all-angles the program is taking too much of time. All the other constraint parameters are default.(running for more than 30 hours). Can any one suggest me that what may be the problem. Regards Harpreet Singh _ Your smile counts. The more smiles you share, the more we donate. Join in. www.windowslive.com/smile?ocid=TXT_TAGLM_Wave2_oprsmilewlhmtagline energyMin.mdp Description: Binary data speptide5.gro Description: Binary data ___ 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] problem in g_confrms
Dear sir, I am trying to fit two confomations of a protein using g_confrms command. The program is giving the result but when I am trying to use two different proteins it is giving the following error. command: g_confrms -f1 1prg.pdb -f2 speptide.pdb -o fit.pdb --- Then it asked to Select group from first structure and Select group from second structure, then I gave 0 (System) for both. At the end it has shown the following error: --- Program g_confrms, VERSION 3.3.1 Source code file: gmx_confrms.c, line: 467 Fatal error: You selected groups with differen number of atoms. --- While in the manual it is mentioned that we can use PDB files with different atoms. Kindly help me regarding this. Regards Harpreet Singh _ Climb to the top of the charts! Play Star Shuffle: the word scramble challenge with star power. http://club.live.com/star_shuffle.aspx?icid=starshuffle_wlmailtextlink_oct___ 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] Using h-angles taking to much time
Dear Sir, I am sorry I missed the information. The problem was while using grompp. Force field used is g34a1 and operating system is Linux. Regards Date: Sat, 20 Oct 2007 08:38:19 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] Using h-angles taking to much time harpreet singh wrote: Dear Sir, I am running Molecular dynamics simulation. Using other constraints the program is running very fast but if I am using constraints = h-angles or all-angles the program is taking too much of time (running since last 12 hours). Kindly suggest me that is it the normal behavior of the program or something went wrong with my data. maybe, maybe not. it would have been helpful if you specified that the problem was in grompp. which force field are you using? which OS and compiler? Regards -niceint 0 Set the nicelevel -[no]v boolyes Be loud and noisy -time real -1 Take frame at or first after this time. -npint 1 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmvsbds boolyes Remove constant bonded interactions with vi sites -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes aro the string, which should contain a number f each node -maxwarnint 10 Number of warnings after which input proces stops -[no]check14 bool no Remove 1-4 interactions without Van der Waa -[no]renum boolyes Renumber atomtypes and minimize number of atomtypes creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 turning all bonds and H angles into constraints... Help yourself to FREE treats served up daily at the Messenger Café. Stop by today! http://www.cafemessenger.com/info/info_sweetstuff2.html?ocid=TXT_TAGLM_OctWLtagline ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Boo! Scare away worms, viruses and so much more! Try Windows Live OneCare! http://onecare.live.com/standard/en-us/purchase/trial.aspx?s_cid=wl_hotmailnews___ 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] Using h-angles taking to much time
Dear Sir, I am running Molecular dynamics simulation. Using other constraints the program is running very fast but if I am using constraints = h-angles or all-angles the program is taking too much of time (running since last 12 hours). Kindly suggest me that is it the normal behavior of the program or something went wrong with my data. Regards -niceint 0 Set the nicelevel -[no]v boolyes Be loud and noisy -time real -1 Take frame at or first after this time. -npint 1 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmvsbds boolyes Remove constant bonded interactions with vi sites -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes aro the string, which should contain a number f each node -maxwarnint 10 Number of warnings after which input proces stops -[no]check14 bool no Remove 1-4 interactions without Van der Waa -[no]renum boolyes Renumber atomtypes and minimize number of atomtypes creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 turning all bonds and H angles into constraints... _ Help yourself to FREE treats served up daily at the Messenger Café. Stop by today. http://www.cafemessenger.com/info/info_sweetstuff2.html?ocid=TXT_TAGLM_OctWLtagline___ 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] regarding g_energy
I am using the g_energy command as follows:1) g_energy -f ener.edr -o output.xvg2) Enter3) 12 04) EnterAfter this the program is doing nothing and only the cursor seems to blink even for hours.Kindly Guide meRegardsHarpreet Singh _ Don't get caught with egg on your face. Play Chicktionary! http://club.live.com/chicktionary.aspx?icid=chick_wlmailtextlink___ 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] invalid order of directive moleule type
Thanks for the valueable suggessions, but sir i am actually want to use this program for small molecules. I have taken single FAD molecule as u suggested modified the atom type as described in ffgmx.rtp, program results top and gro files using pdb2gmx, but while running grompp i am getting the error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 1284 of the 1485 non-bonded parameter combinations WARNING 1 [file fad.top, line 128]: No default Bond types, using zeroes WARNING 2 [file fad.top, line 139]: No default Bond types, using zeroes WARNING 3 [file fad.top, line 141]: No default Bond types, using zeroes WARNING 4 [file fad.top, line 328]: No default Angle types, using zeroes WARNING 5 [file fad.top, line 329]: No default Angle types, using zeroes WARNING 6 [file fad.top, line 334]: No default Proper Dih. types, using zeroes WARNING 7 [file fad.top, line 336]: No default Proper Dih. types, using zeroes WARNING 8 [file fad.top, line 338]: No default Proper Dih. types, using zeroes WARNING 9 [file fad.top, line 341]: No default Proper Dih. types, using zeroes WARNING 10 [file fad.top, line 343]: No default Proper Dih. types, using zeroes Cleaning up temporary file gromppLLm3l8 --- Program grompp, VERSION 3.3.1 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp terminated --- I Need Love, Not Games (Iggy Pop Kate Pierson) Moreover , suppose if we want to use this program (grompp) for say, a molecule which has no entry in any .rtp file provided with Gromacs and we use the PRODRG server, then how to deal with the error invalid molecular directive type. Kindly explain me regarding this error in detail, if you can spare some time for me. If you want i can give the sample files for what i am trying to do. Thanks From: merc mertens [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] invalid order of directive moleule type Date: Tue, 07 Nov 2006 13:00:02 +0100 if i were you, i would rather adapt my pdb file to an existing forcefield as ffgmx, than trying to generate a new forcefield that fits to your pdb with prodrug. the first option seems much easier to me. what i mean is, if you change the names of you FAD atoms to the ones you see in the *rtp they will be recognized by pdb2gmx. Original-Nachricht Datum: Tue, 07 Nov 2006 11:35:47 + Von: harpreet singh [EMAIL PROTECTED] An: gmx-users@gromacs.org Betreff: [gmx-users] invalid order of directive moleule type Hi All, I am new to this package and want your help. I am trying to use GROMACS to study energy minimization and molecular dynamics for FAD molecule. I am having the following problems. 1. I tried to run pdb2gmx for PDB file for FAD downloaded from http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl site. and used the gromacs force field . The program gave the following error: - Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.hdb Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx-n.tdb Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx-c.tdb Back Off! I just backed up fad_test.top to ./#fad_test.top.1# Processing chain 1 (53 atoms, 1 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds --- Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2gmx.c, line: 393 Fatal error: Atom O1P in residue FAD 1 not found in rtp entry with 61 atoms while sorting atoms On comparing topology file (ffgmx.rtp) for FAD entry i was surpried to see that it has atom type enteries OP1, OP2 instead of O1P, O2P in downloaded PDB file (fad.pdb). Also atom type at number 23 was O in ffgmx.rtp (for FAD) and O3P was missing in this file. I am attaching the files herewith. 2. I tried to make .top and .gro files (fad92.top and fad.gro respectively) ,using PRODRG2 server. and used them with grompp commad grompp -f em.mdp -c fad92.gro -p fad92.top -o fad92.tpr This resulted in the following error. Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Cleaning up temporary file gromppfYcUxi --- Program grompp, VERSION 3.3.1 Source code file: topio.c, line: 388 Fatal error: Invalid order for directive moleculetype, file fad92.top, line 15 --- Oh, There Goes Gravity (Eminem) Kindly guide me to solve this problem. Thanks in advance Harpreet Singh
[gmx-users] invalid order of directive moleule type
Hi All, I am new to this package and want your help. I am trying to use GROMACS to study energy minimization and molecular dynamics for FAD molecule. I am having the following problems. 1. I tried to run pdb2gmx for PDB file for FAD downloaded from http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl site. and used the gromacs force field . The program gave the following error: - Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.hdb Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx-n.tdb Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx-c.tdb Back Off! I just backed up fad_test.top to ./#fad_test.top.1# Processing chain 1 (53 atoms, 1 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds --- Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2gmx.c, line: 393 Fatal error: Atom O1P in residue FAD 1 not found in rtp entry with 61 atoms while sorting atoms On comparing topology file (ffgmx.rtp) for FAD entry i was surpried to see that it has atom type enteries OP1, OP2 instead of O1P, O2P in downloaded PDB file (fad.pdb). Also atom type at number 23 was O in ffgmx.rtp (for FAD) and O3P was missing in this file. I am attaching the files herewith. 2. I tried to make .top and .gro files (fad92.top and fad.gro respectively) ,using PRODRG2 server. and used them with grompp commad grompp -f em.mdp -c fad92.gro -p fad92.top -o fad92.tpr This resulted in the following error. Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Cleaning up temporary file gromppfYcUxi --- Program grompp, VERSION 3.3.1 Source code file: topio.c, line: 388 Fatal error: Invalid order for directive moleculetype, file fad92.top, line 15 --- Oh, There Goes Gravity (Eminem) Kindly guide me to solve this problem. Thanks in advance Harpreet Singh _ Use your PC to make calls at very low rates https://voiceoam.pcs.v2s.live.com/partnerredirect.aspx ___ 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
