[gmx-users] trjconv -conect

[Justin A. Lemkul]

On 5/27/12 4:58 PM, vijaya subramanian wrote:
> So how do people use trjconv -conect? It says in the manual it is useful for cg
> results-
>

Most Gromacs programs assume that you have Gromacs input files at your disposal. 
  A .tpr file is a simulation input file and thus is accessible to anyone who 
has done MD via mdrun.

In your case, it is relatively easy to copy and paste the CONECT records from 
your existing file(s), as Tsjerk suggested.

-Justin

>  > Date: Sun, 27 May 2012 13:39:48 -0400
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] trjconv -conect
>  >
>  >
>  >
>  > 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: jalemkul at vt.edu
>  > > > To: gmx-users at gromacs.org
>  > > > 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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-- 
========================================

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

========================================