Re: [gmx-users] Re: Re: topology using prodrg (Diego Nolasco)
Take a look at John Kerrigan's tutorial? http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf And as said Justin, There is no mention of Gromos87 in the topology line. Diego. 2008/7/6 h a [EMAIL PROTECTED]: Yea I used the beta version and chose the force field GROMOS96.1. But after I run the server I get this output Output example for the input thf.pdb * PRODRG Starting up PRODRG version AA080107.0543 PRODRG Parameter set 'pd/gromos96' (fftype=2). PRODRG PDB mode detected. PRODRG WARNING: deleted hydrogen(s) from your input. PRODRG Molecule complexity index: 2.00. PRODRG 8 hydrogen(s) added. PRODRG Using charge groups. PRODRG Net charge on molecule: 0.000 PRODRG 9 partial charges 0 ambiguous PRODRG 13 bonds0 ambiguous PRODRG 25 bond angles 8 ambiguous PRODRG 4 improper dihedrals 0 ambiguous PRODRG 5 dihedrals0 ambiguous PRODRG Writing GROMACS topology. PRODRG GROMACS topology quality on 0-10 scale: 7.8 GENDRG Best structure was iteration 3211 with 3.20067739 PRODRG Spawning GROMACS version 3.3.3... PRODRG RMSD from GROMOS bond ideality (Angstrom) : 0.003 PRODRG RMSD from GROMOS angle ideality (degrees) : 2.895 PRODRG RMSD from GROMOS plane ideality (degrees) : 5.553 PRODRG Number of improper improper dihedrals : 0 PRODRG RMSD from starting bonds (Angstrom) : 0.011 PRODRG RMSD from starting angles (degrees) : 0.464 PRODRG RMSD from starting planes (degrees) : 0.000 PRODRG RMSD from starting coords (Angstrom) : 0.012 PRODRG Writing: SCRTHOWMMPG PRODRG Normal program end. Click to go to the following output: Coordinates # PDB (all H's [D][V], polar/aromatic H's [D][V], polar H's only [D][V] or no H's [D][V]) # MDL Molfile (all H's [D][V], polar H's only [D][V] or no H's [D][V]) # GROMOS87/GROMACS (all H's [D], polar/aromatic H's [D] or polar H's only [D]) . . . . . The GROMOS87/GROMACS coordinate file (polar/aromatic hydrogens) . . . . . The GROMOS87/GROMACS coordinate file (all hydrogens) . . . The GROMACS topology . . . . . * It says that parameter set 'pd/gromos96' (in second line) but output was gromos87 coordinate files, topology files :( . can anybody explain why did this happen ? am I missing anything ? thank you, harshith Are you sure you used prodrg beta? http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta 2008/7/4, h a [EMAIL PROTECTED]: Dear users, I am modeling polymer surface. I need topology for polystyrene. I used prodrg earlier version and beta version but in both cases I get topology for only GROMOS87 force field. Can not I get topology for force filed GROMOS96 ? also can anybody let me know what is .itp file for GOMOS87 force filed ( I mean similar to GROMOS96 - ffG43a1.itp ) thank you, Sincerely --- A.Harshith(Y6001) department of Bio Science and Bioengineering, IIT Kanpur, India. http://home.iitk.ac.in/~harshith http://home.iitk.ac.in/%7Eharshith http://home.iitk.ac.in/%7Eharshith ___ 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] topology using prodrg
Are you sure you used prodrg beta? http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta 2008/7/4, h a [EMAIL PROTECTED]: Dear users, I am modeling polymer surface. I need topology for polystyrene. I used prodrg earlier version and beta version but in both cases I get topology for only GROMOS87 force field. Can not I get topology for force filed GROMOS96 ? also can anybody let me know what is .itp file for GOMOS87 force filed ( I mean similar to GROMOS96 - ffG43a1.itp ) thank you, Sincerely --- A.Harshith(Y6001) department of Bio Science and Bioengineering, IIT Kanpur, India. http://home.iitk.ac.in/~harshith http://home.iitk.ac.in/%7Eharshith ___ 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] topology for c-alpha protein model
After pdb2gmx of the whole structure, make an index file and them run another pdb2gmx choosing the c-alpha group. I hope it helps. 2008/6/20, Lillian Chong [EMAIL PROTECTED]: Dear Gromacs Users, I would like to generate a topology for a protein in which each residue is represented only by its C-alpha atom (a Go-type model). What would be the most straightforward way of creating this topology file? Thanks in advance, Lillian ___ 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] REMD problems
Thank you very much Marcus and Berk, it's running!!! 2008/6/6, Marcus Kubitzki [EMAIL PROTECTED]: Hi Diego, during initialization of an REMD run, GMX checks if certain properties are equal among replicas. If not, this incompatibility errors occurs. Check the log files, for there is written what is not identical in one of your replicas. Look for XXX is not equal for all subsystems Marcus Diego Nolasco wrote: Dear gmx-users, I am facing some problems with replica exchange. Few seconds after the job submission it ends with the error below: Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 8 --- Program mdrun, VERSION 3.3.3 Source code file: main.c, line: 177 Fatal error: The 8 subsystems are not compatible I am using a single topology for all configurations, but it still doesn't work. Does anyone have any tip over this problem? Thanks in advance, Diego. ___ 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 -- Dr. Marcus Kubitzki Max Planck Institute for Biophysical Chemistry Computational Biomolecular Dynamics Group Am Fassberg 11 D-37077 Göttingen Germany phone: ++49-551-2012312 fax: ++49-551-2012302 Email: mkubitz[at]gwdg.de www: http://www.mpibpc.mpg.de/groups/de_groot/ ___ 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] REMD problems
Dear gmx-users, I am facing some problems with replica exchange. Few seconds after the job submission it ends with the error below: Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 8 --- Program mdrun, VERSION 3.3.3 Source code file: main.c, line: 177 Fatal error: The 8 subsystems are not compatible I am using a single topology for all configurations, but it still doesn't work. Does anyone have any tip over this problem? Thanks in advance, Diego. ___ 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] how to run parallel jobs in gromacs
Hi there, Try giving the complete address of the command you want to run, just like this: /usr/bin/grompp -f *.mdp -c *.gro -p *.top -o *.tpr -np 4 mpirun -np 4 /usr/bin/mdrun_mpi.lam -s *.tpr -x *.xtc -c *.gro -g *.log -e *.edr -v The address depends on your installation. In my case is /usr/bin/. I hope it helps, Diego. 2007/8/6, Anupam Nath Jha [EMAIL PROTECTED]: Dear all i am new in gromacs. i have installed gromacs-3.3.3 in our cluster(mpi is already there) with parallel version (using the following command): make clean ./configure --enable-mpi --disable-nice --program-suffix=_mpi make mdrun make install-mdrun it went fine. but when i ran the command - qsub pbs_submit it's the pbs_submit file: #This is a PBS script for Parallel Jobs #!/bin/bash -f #PBS -l nodes=2:ppn=2 #PBS -o /home/anupam/MD/lyd #PBS -e /home/anupam/MD/lyd #PBS -q default cd /home/anupam/MD/lyd mpirun grompp -f em.mdp -p topol.top -c solvated.gro -np 4 -o em.tpr mpirun mdrun_mpi -v -deffnm -np 4 em but it's not doing anything,except writing this: totalnum=3 numhosts=2 there are not enough hosts on which to start all processes totalnum=3 numhosts=2 there are not enough hosts on which to start all processes can you help me out? thanks in adavnce anupam -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily sciece. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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] FEP method in protein-ligand systems
Thank you David, I really appreciated your help. I will read your paper and try to go on. Thank you very much! 2007/7/27, David Mobley [EMAIL PROTECTED]: Hi, I am trying to run some simulations in attempts to calculate binding free energy between ligands and a protein using the FEP method, but until now I did not have any success. I have been looking for bibliography over this subject, but, as you may know, there aren't many works about FEP. What I found is one job where the solvation of amino acids analogs was calculated, but there wasn't any mention about the usage of the method in protein-ligand systems. What I would like to ask is: Is it possible to develop work over free energy calculations using the FEP method in protein-ligand systems? You might start with my recent JMB paper for references. http://dx.doi.org/10.1016/j.jmb.2007.06.002. There are also recent reviews of free energy calculations by Rodinger and Pomes, and by David Kofke, as well as one by Michael Shirts, myself, and John Chodera that will be out in Annual Reports in Computational Chemistry that will be out soon. For that matter, any literature search on free energy perturbation should turn up lots of hits. I get 2,600 in a Google scholar search on the subject ( http://scholar.google.com/scholar?hl=enlr=q=%22free+energy+perturbation%22btnG=Search ). Lots of hits for alchemical free energy calculations and thermodynamic integration as well. I'm not sure why you think there aren't many publications on FEP. David Thanks a lot, Diego Nolasco ___ 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 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
