Liu Shiyong wrote:
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.
The .gro file format does not permit chain identifiers. So they were
lost when you wrote ${file}.gro, and re-invented for output.pdb. If I
remember correctly they're also not stored in a .tpr file.
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.
There's no way to fix this one with GROMACS (at least, as far as I
know). However if you edit your starting.pdb file to have the same kind
of format as output.pdb, then you can use the standard unix utility
programs head, tail, grep, cut and paste to solve this problem. Use
head -n x output.pdb > head
tail -n y output.pdb > tail
to extract the header and footer to separate files, and then grep out
all of the lines that begin with atom records
grep -e '^ATOM' output.pdb > outputatom
grep -e '^ATOM' starting.pdb > startingatom
Then
cut -c=z startingatom > chainidentifiers
cut -c-1-a outputatom > left
cut -c=b- outputatom > right
paste -d='' left chainidentifiers right > middle
cat head middle tail > fixed.pdb
and to clean up
rm head tail outputatom startingatom chainidentifiers middle
You will need to identify the correct numbers for x, y, and z, and a=z-1
and b=z+1. See the man pages for each of these commands to learn more.
Mark
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