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

Alan alanwilter at gmail.com
Wed Aug 25 17:52:42 CEST 2010

Ah, great. Thanks Berk.

FYI, because I am developing a tool (ACPYPE) and I wrote the test using
gromacs and ff oplsaa and amber so that's why it's relatively easy and quick
to test and check the issues I was having. But it also happens that I am
adapting my test code for gmx 4.5 and so I bump in some problems, 99% my
fault of course.

Thanks a lot for your prompt replies.



On 25 August 2010 16:06, Berk Hess <gmx3 at hotmail.com> wrote:

>  Hi,
> 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.
> Berk
> ------------------------------
> 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
> 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:
> share/top/amber99.ff/aminoacids.r2b
> 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?
> Berk
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Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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