Hi, all,
I used ambpdb to generate pdb and pqr files from .prmtop (there is chain ID information) and .inpcrd file, and find that options "-ext" and "-pqr" of ambpdb are exlusive.
If I only use "-ext", the output pdb file include chain ID information.
ambpdb -p 1EMVAB.prmtop -aatm -bres -ext <1EMVAB.inpcrd >ambpdb.pdb
ATOM 1 N LEU A 1 -1.254 -0.651 68.866 1.00 0.00 N
ATOM 2 H1 LEU A 1 -0.409 -0.606 68.314 1.00 0.00 H
ATOM 3 H2 LEU A 1 -1.209 -1.464 69.464 1.00 0.00 H
ATOM 4 H3 LEU A 1 -1.430 0.260 69.265 1.00 0.00 H
...
But when I use "-ext -pqr", the output pqr file does NOT include chain ID information!
ambpdb -p 1EMVAB.prmtop -pqr -aatm -bres -ext <1EMVAB.inpcrd >ambpdb.pqr
ATOM 1 N LEU 1 -1.254 -0.651 68.866 0.1010 1.550 N
ATOM 2 H1 LEU 1 -0.409 -0.606 68.314 0.2148 1.200 H
ATOM 3 H2 LEU 1 -1.209 -1.464 69.464 0.2148 1.200 H
ATOM 4 H3 LEU 1 -1.430 0.260 69.265 0.2148 1.200 H
...
However, what I need is a pqr file with chain ID information! So I have to merge the two files by hand. :(
I hope the two options can coexist.
Best,
Anbang------------------
Physics Department, Central China Normal University, China
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Received on Tue Nov 11 2014 - 20:00:02 PST
