Hi,<br><br>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.<br>But the chain name was changed. I checked the man trjconv , but I did not find any information on chain name for trjconv. <br>
<br>pdb2gmx -ff ${forcefield} -f starting.pdb -p ${file}.top -i ${file}.posre.itp -o ${file}.gro > ${file}.output.pdb2gmx 2>&1<br><br>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<br>
<br>trjconv -sep -f ${file}.minim_traj.trr -s ${file}.input.tpr -o output.pdb << HHH<br>2<br>2<br>HHH<br><br>The starting.pdb has four chain: A B D E<br>The output file output.pdb has a different chain name: A B C D.<br>
<br>Thanks<br><br clear="all"><br>-- <br>Shiyong Liu<br>Research Assistant<br>center for bioinformatics in the university of kansas<br>Lab: (785)864-1962<br>Email: <a href="mailto:syliu@ku.edu">syliu@ku.edu</a> (<a href="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</a> or <a href="mailto:liushiyong@ku.edu">liushiyong@ku.edu</a>)<br>
Homepage: <a href="http://www.people.ku.edu/~syliu">http://www.people.ku.edu/~syliu</a><br>Lab: <a href="http://vakser.bioinformatics.ku.edu/people">http://vakser.bioinformatics.ku.edu/people</a><br>Phone: (785) 864-1962