From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu May 01 2008 - 00:15:28 CDT
The reason it doesn't exist in the topology is because it's quite rare. I
don't know if a topology exists for it somewhere (chances are someone has
done it before), but like you suggest, it could be created pretty simply,
analogous to what's done for LYS.
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Alexandre F. G.
Sent: Tuesday, April 29, 2008 4:45 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Neutral arginine patch in topology file.
Dear all,
I'm running some MD calculations with non-solvated peptides (~14 residues)
and different charge states/protonation sites, and I want to be able to do
them with neutral arginine residues. The topology file I'm using
(top_all27_prot_lipid.inp) contains a patch (PRES) for neutral lysine (LSN
instead of LYS), but not for neutral arginine.
Does anyone know if such a patch exists somewhere or, if not, how to create
one? Considering I had the charge distributions for a neutral arginine
residue, would it be appropriate to just replace the charge distributions
and remove the extra hydrogen atom when writing the patch code?
Thank you very much,
Alexandre F. Gomes
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