Re: Generating a gromacs topology file for analyzing NAMD trajectories

From: Ilya Chorny (ichorny_at_gmail.com)
Date: Wed Dec 05 2007 - 16:13:31 CST

Does anyone know what to do when Gromacs requires a tpr file?

On Dec 5, 2007 1:25 PM, Giovanni Bellesia <gbellesia_at_chem.ucsb.edu> wrote:

> Hi,
> I used once the GROMACS g_covar tool converting first my dcd file to
> trr with catdcd and using a pdb file as the Structure+mass input file .
> In details:
>
> catdcd -o myfile.trr -otype trr myfile.dcd
> g_covar -f myfile.trr -s mypdb.pdb
>
> Giovanni
> > Hi.
> >
> > I'm trying to use gromacs to do PCA on a trajectory I generated using
> > NAMD. This requires a .top file.
> >
> > So far, I tried using 1 frame of my trajectory (saved as a pdb file) I
> > aliased HSE back to HIS and ILE CD back to CD1. Nevertheless, the
> > program pdb2gmx (for making gromacs files) keeps running into atom
> > types that it can't recognize (this even happens when I use the
> > "ignore hydrogens" option).
> >
> > I could start from the original pdb from the protein data bank, but
> > wouldn't this generate a .top file that would be incompatible with the
> > trajectory?
> >
> > Has anyone successfully used gromacs to do PCA of a NAMD trajectory?
> > If so, how did you generate your .top file?
> >
> > Thanks.
> >
> > Patrick L. Wintrode
> > Dept. of Physiology & Biophysics
> > Case Western Reserve University
> > Cleveland, OH 44106
>
>

-- 
Ilya Chorny Ph.D.

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