Hi,
I can think of a temporary workaround using cpptraj:
parm 1EMVAB.prmtop
trajin 1EMVAB.inpcrd
trajout ambpdb.pdb pdb pdbv3 dumpq chainid A
Note that this will give everything the same chain ID ('A'). However,
you could potentially use actual chain IDs from another PDB in a
second pass (if that PDB that matches your topology).
Hope this helps,
-Dan
On Tue, Nov 11, 2014 at 8:48 PM, LI An-Bang <anbangli.qq.com> wrote:
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Nov 12 2014 - 07:30:02 PST
