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
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: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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