Phosphorylated Residues

From: Oscar Bastidas (obastida_at_umn.edu)
Date: Tue Jun 26 2018 - 23:29:07 CDT

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

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