Dear users, If I obtain/generate the topology file for a ligand using another program (except PRODRG);
1) How can I arrange .itp file? Because it seems very complicate. 2) Justin tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html We will make use of two files that PRODRG gives us. Save the output of the field "The GROMOS87/GROMACS coordinate file (polar/aromatic hydrogens)" into a text file called "jz4.gro" and "The GROMACS topology" into a file called "drg.itp." Then how can I generate .gro file using another program? I was obtaining .gro and .itp files using PRODRG but PRODRG is giving improper results/output. best regards 2011/9/17 Mark Abraham <mark.abra...@anu.edu.au> > On 17/09/2011 11:28 PM, ahmet yıldırım wrote: > >> Dear Tsjerk and Justin, >> >> Thanks for your reply. I will contact the PRODRG developers. >> can you suggest anyway/anytool for generating ligand >> coordinates/topologies? >> > > http://www.gromacs.org/**Documentation/How-tos/Steps_** > to_Perform_a_Simulation<http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation> > > Mark > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet YILDIRIM
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