[gmx-users] trjconv chaged the chain names of multi-chain complex?

[Justin A. Lemkul]

Quoting Liu Shiyong <liushiyong at gmail.com>:

> Hi,
>
> Chain name is very important for some application.  But,  when I  use the
> following script to get a minimized structure from a multi-chain  complex.
> But the chain name was changed.  I checked the man trjconv , but I did not
> find any information on chain name for trjconv.
>
> pdb2gmx   -ff ${forcefield} -f  starting.pdb -p ${file}.top -i
> ${file}.posre.itp -o ${file}.gro > ${file}.output.pdb2gmx 2>&1

Check the pdb2gmx output; I suspect the renaming happened here.  If that is the
case, some simple work with a text editor should fix the problem.

-Justin

>
> mdrun -nice 0 -v -s ${file}.input.tpr -o ${file}.minim_traj.trr -c
> ${file}.minimized.gro -e ${file}.minim_ener.edr -g ${file}.emlog.log    >
> ${file}.output.mdrun 2>&1
>
> trjconv  -sep -f ${file}.minim_traj.trr -s ${file}.input.tpr -o output.pdb
> << HHH
> 2
> 2
> HHH
>
> The starting.pdb has four chain: A B  D E
> The output file output.pdb has a different chain name: A B C D.
>
> Thanks
>
>
> --
> Shiyong Liu
> Research Assistant
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
> Homepage: http://www.people.ku.edu/~syliu
> Lab: http://vakser.bioinformatics.ku.edu/people
> Phone: (785) 864-1962
>



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Justin A. Lemkul
Graduate Research Assistant
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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