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. Best, Alan On 25 August 2010 16:06, Berk Hess <[email protected]> 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: [email protected] > Date: Wed, 25 Aug 2010 15:39:13 +0100 > > Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now > To: [email protected] > > 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 <[email protected]> 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 > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<<
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