Re: Phosphorylated Residues

From: Aysima Hacisuleyman (
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 <> wrote:

> Hello,
> 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!
> Oscar
> Sent from my uPad

*Aysima Hacısüleyman*
*PhD Candidate*
*Chemical and Biological Engineering*
*Koc University, Sarıyer, Istanbul, TURKEY*

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