tleap does not preserve this information. You can use the program
"add_pdb" that's distributed with AmberTools to add PDB information (you
need the original PDB file). That will generate a prmtop file with the PDB
information in it. ambpdb may then be able to generate the PDB file with
preserved information for you, but I'm not sure. All of these programs are
described in the manual.
HTH,
Jason
On Wed, Jan 30, 2013 at 5:59 AM, aneesh cna <aneeshcna.gmail.com> wrote:
> Dear Amber users,
>
> I am using tleap for adding the missing atoms in a PDB file. I used the
> following command the same.
>
> source leaprc.ff99SB
> MM = loadpdb Y.pdb
> savepdb MM Y_leap.pdb
> quit
>
>
> Unfortunately, savepdb command generate the new pdb file without having the
> chain ID information in it. Since the protein is a multimer, I want to keep
> the chain ID, which is present in the original pdb file, in the newly
> generated pdb file. Is there a way to retain the chain ID in the new PDB
> file?
>
>
> Waiting for your valuable reply
>
>
> Thanks in advance
>
> Best regards,
> Aneesh
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jan 30 2013 - 05:00:03 PST
