[gmx-users] query regarding itp file

Mark Abraham mark.j.abraham at gmail.com
Tue May 19 14:50:44 CEST 2015


You can easily generate position restraints files yourself - have a look at
one and learn about the column format from chapter 5. There is also gmx
genrestr to help with this - but read the documentation first.


On Tue, May 19, 2015 at 2:10 PM soumadwip ghosh <soumadwipghosh at gmail.com>

> Hi all,
>        I have some general doubts about the use of an itp file built by
> some software. I am studying the dynamics of a DNA in presence of a
> graphene sheet. I am using now the CHARMM27 force field and have obtained a
> graphene.itp file from PARAMCHEM where the atom types of the sp2 carbon
> atoms and the terminal hydrogen atoms of the graphene sheet have been taken
> into account according to the standard CHARMM directory. Now, do I need to
> modify my aminoacids.rtp file in order to account for the atoms in the PDB
> file? I have not done any pdb2gmx so do I really need to do that step? The
> atom types in the .itp file provided by the PARAMCHEM has CA and HP atoms
> which describe the graphene framework in addition to other non-bonded
> parameters. The equilibration steps are running without any hitches but I
> am not getting whether the proper interaction (atomistic) would arise
> between graphene and DNA atoms. As suggested by Justin i've switched over
> to CHARMM27 force field and am looking at atlest 200 ns of production run.
> Another question is, since I have not performed pdb2gmx on graphene, I dont
> have a posre_graphene file. Is it gonna create some problem later during
> mdrun? I will be grateful if someone clarifies my doubts. Can I get a posre
> file for graphene by some other method without doing pdb2gmx if this file
> is mandatory?
> Hope I'm not asking for much.
> Regards,
> Soumadwip
> Research Fellow
> IIT Bombay
> India
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