[gmx-users] trjconv -conect

[Justin A. Lemkul]

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

-- 
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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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