Re: Phosphorylated Residues

From: Aysima Hacisuleyman (ahacisuleyman_at_ku.edu.tr)
Date: Wed Jun 27 2018 - 05:54:02 CDT

Hello,

You can use toppar_prot_na_all.str (you can find it in
http://mackerell.umaryland.edu/charmm_ff.shtml
<https://www.researchgate.net/deref/http%3A%2F%2Fmackerell.umaryland.edu%2Fcharmm_ff.shtml>
), it includes all the patches for phosphorylated residues. Here you can
find a short NAMD tutorial (
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node24.html
<https://www.researchgate.net/deref/http%3A%2F%2Fwww.ks.uiuc.edu%2FTraining%2FTutorials%2Fnamd%2Fnamd-tutorial-unix-html%2Fnode24.html>)
on using patches found in topology files.

Hope it helps!

Aysima

On Wed, Jun 27, 2018 at 7:29 AM, Oscar Bastidas <obastida_at_umn.edu> 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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