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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