For example if I have a polystyrene polymer chains and monomers of user defined solvent . I need to construct the .itp file by hand .
Thanks for the reply Kirtana On Tue, Feb 28, 2012 at 5:31 PM, Justin A. Lemkul <[email protected]> wrote: > > > kirtana S wrote: > >> Dear Users, >> >> In the gromacs manual on means to convert the pdb file to gromacs >> topology file I need to use pdb2gmx. Here I have to specify the force field >> .How to work with organic residues which do not exists . Since I had used >> general amber force field, and could not find this in the /share/top/ >> directory . Do I need to manually construct the .itp file for each >> residues. What will be the easiest way to construct >> a solvated box with user defined residues in gromacs. >> >> > If the residue of interest will be a component of a polymeric molecule > like a protein, refer to http://www.gromacs.org/** > Documentation/How-tos/Adding_**a_Residue_to_a_Force_Field<http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field>. > If the molecule is a standalone species like a ligand, solvent, etc then > all you have to do is #include an .itp file in the system topology. > > -Justin > > -- > ==============================**========== > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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