From: Alexandre F. G. (alexandrefgo_at_gmail.com)
Date: Tue Apr 29 2008 - 16:45:29 CDT
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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