[gmx-users] trjconv -conect

[Justin A. Lemkul]

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
>  >
>  > ========================================
>  > --
>  > gmx-users mailing list gmx-users at gromacs.org
>  > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  > Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>  > Please don't post (un)subscribe requests to the list. Use the
>  > www interface or send it to gmx-users-request at gromacs.org.
>  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
========================================

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

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