From: Aysima Hacisuleyman (ahacisuleyman_at_ku.edu.tr)
Date: Wed Jun 27 2018 - 05:54:02 CDT
You can use toppar_prot_na_all.str (you can find it in
), it includes all the patches for phosphorylated residues. Here you can
find a short NAMD tutorial (
on using patches found in topology files.
Hope it helps!
On Wed, Jun 27, 2018 at 7:29 AM, Oscar Bastidas <obastida_at_umn.edu> wrote:
> I want to set up a NAMD simulation of a system containing phosphorylated
> residues by prepping my files through VMD's Automatic PSF Builder.
> According to a resource I found, the topology file toppar_all36_prot_na_
> combined.str care of CHARMM-GUI, addresses these PTMs but when I
> incorporate this file into the Automatic PSF Builder alone, I get error
> messages upon trying to split the chains. What topology files should I use
> in the Auto. PSF Builder to move forward? I tried using both the
> afforementioned topology file and the standard top_all27_prot_lipid.inp
> file from the basic NAMD tutorial but had no luck either.
> Word of note, I looked through the mailing list archives (keywords:
> phosphorylated residue) and although someone asked a very similar question
> on June 25, 2008, no one ever responded to that inquiry.
> Thanks and I hope someone can steer me in the right direction!
> Sent from my uPad
-- *Aysima Hacısüleyman* *PhD Candidate* *Chemical and Biological Engineering* *Koc University, Sarıyer, Istanbul, TURKEY*
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