On 5/27/12 1:36 PM, vijaya subramanian wrote:
Hi
I don't have a .tpr file for the cg system. I am anlayzing results from pca and
the trajectories only have calpha atoms.
Can I generate a .tpr for just calpha?
Not without your own custom force field. No Gromacs force field is compatible
with CA-only models. There are a few scripts on the User Contribution site that
may be useful.
-Justin
> Date: Sun, 27 May 2012 12:12:14 -0400
> From: [email protected]
> To: [email protected]
> Subject: Re: [gmx-users] trjconv -conect
>
>
>
> On 5/27/12 12:05 PM, vijaya subramanian wrote:
> >
> > Hi
> > I am trying to add conect records to a cg trajectory under gromacs 4.5.4 as
follows:
> > trjconv -s CONECT.PDB -f traj.xtc -conect -o testconect.pdb
> >
> > or with one frame
> >
> > trjconv -s CONECT.PDB -f oneframe.pdb -conect -o testconect.pdb
> >
> > but dont see any conect records in the output file.
> >
> > The conect records are in the input to -s , conect.pdb and in the following
format:
> > ...
> > ATOM 4125 CA HIS X 173 107.816 143.564 71.946 1.00 0
> > ATOM 4126 CA THR X 174 110.288 142.372 69.327 1.00 0
> > ATOM 4127 CA LEU X 175 111.958 139.227 70.607 1.00 0
> > ATOM 4128 CA GLY X 176 108.771 138.107 72.357 1.00 0
> > CONECT 1 2
> > CONECT 2 3
> > CONECT 3 4
> > CONECT 4 5
> > CONECT 5 6
> > CONECT 6 7
> > CONECT 7 8
> > CONECT 8 9
> > CONECT 9 10
> > CONECT 10 11
> > CONECT 11 12
> > CONECT 12 13
> > CONECT 13 14
> > CONECT 14 15
> > CONECT 15 16
> > CONECT 16 17
> > CONECT 17 18
> > CONECT 18 19
> > CONECT 19 20
> > CONECT 20 21
> > CONECT 21 22
> > ...
> >
> > What should I do differently to get the conect records in the output file?
> >
> >
>
> Try using a .tpr file, where bonds are present according to the topology.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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