[gmx-users] trjconv -conect

[Justin A. Lemkul]

On 5/27/12 5:03 PM, vijaya subramanian wrote:
> one conect record for all models?

You need the CONECT records for visualization, right?  Or is there some other 
purpose?  In theory, if you have one .pdb file with CONECT records, you can load 
your trajectory as data for it and the bonds should be preserved.

I'm also curious how you have a Gromacs .xtc file without having a .tpr file. 
Did you not run the simulation and/or analysis with Gromacs?

-Justin

> thanks-
> --------------------------------------------------------------------------------
> Date: Sun, 27 May 2012 20:24:59 +0200
> Subject: Re: [gmx-users] trjconv -conect
> From: tsjerkw at gmail.com
> To: jalemkul at vt.edu; gmx-users at gromacs.org
> CC:
>
> Hi Vijaya,
> Just copy the CONECT records from the reference pdb afterwards.
> Cheers,
> Tsjerk
>
>     On May 27, 2012 7:42 PM, "Justin A. Lemkul" <jalemkul at vt.edu
>     <mailto:jalemkul at vt.edu>> wrote:
>
>     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 trajectorie...
>
>
>     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
>         <mailto:jalemkul at vt.edu> > > To: gmx-users at gromacs.org...
>          > > On 5/27/12 12:05 PM, vijaya subramanian wrote: > > > > > > Hi > > >
>         I am trying to add conec...
>
>     -- ======================================== Justin A. Lemkul, Ph.D. Research
>     Scientist Departmen...
>
>
>
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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

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