[gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

Berk Hess gmx3 at hotmail.com
Wed Aug 25 17:06:22 CEST 2010


This is completely unrelated.
Eric changed all the names to allow processing of his ports by Gromacs version 3.3 and 4.0.
In 4.5 I enabled fully rtp name flexibility and I changed all rtp names back to the Amber nomenclature.


From: alanwilter at gmail.com
Date: Wed, 25 Aug 2010 15:39:13 +0100
Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
To: gmx-users at gromacs.org

Not really, I mentioned that based on Sorin's ffamber page:
a)	Non-terminal amino and nucleic acid residues follow standard AMBER naming conventions. To avoid confusion between GROMACS and AMBER conventions, we have omitted the redundant HIS residue, leaving HID, HIE, HIP, and terminal versions of these topologies. Additionally, due to the automated changing of certain residue names by pdb2gmx, the LYS and CYS residues have been renamed LYP (Lysine plus) and CYN (Cysteine neutral, compared to AMBER residue CYM = Cysteine minus).

(b)	C- and N-terminal amino acids include a C or N prefix respectively, so C-terminal ALA is CALA and N-ternimal PHE is NPHE. As with non-terminal versions, the LYS and CYS terminal residues are listed as NLYP,CLYP and NCYN,CCYN.

And I did mistake, it's not CYP, but CYN.
So I don't know if you are fully following Sorin's recommendations.

On 25 August 2010 14:36, Berk Hess <gmx3 at hotmail.com> wrote:

You can find the residue name to rtp translation table in:

I don't have a list with Amber names and funtions for the amino acids.
Currently for Amber in Gromacs we have CYS (standard, neutral, protonated)

and CYX (disulfide bond).
Does Amber use CYP instead of CYS?

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