Re: [AMBER] problem in adding ACE and NME to CSX.

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 13 Dec 2015 11:28:16 -0500

On Sun, Dec 13, 2015 at 7:58 AM, Saman Yousuf ali <
saman.yousufali64.yahoo.com> wrote:

> Hi, amber users:
> I have a modified cysteine residue CSX (S-Oxy cysteine) in my protein
> target (PDB=3JQ9). I want to add ACE and NME to cap this modified residue
> before Resp charge calculation. Kindly guide me how to cap the protein
> terminal?
>

‚ÄčIf you do not have a residue library file for CSX (either a .lib or
.mol3/.prep file), then there are no Amber programs capable of doing this.
So either create a "dummy" residue template library file for CSX so you can
use the "sequence" command in tleap to build the molecule, or find another
program to do it.

I would personally use Avogadro to draw in the required atoms and do your
charge derivation with that (just make sure to rename the atoms to the PDB
standard, as given in
http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CSX).

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Dec 13 2015 - 08:30:03 PST
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