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

Liu Shiyong liushiyong at gmail.com
Mon Apr 7 22:54:14 CEST 2008


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

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

The starting.pdb has four chain: A B  D E
The output file output.pdb has a different chain name: A B C D.


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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