Hi Maik,
These updated NA params would be nice to add and test, but I've been too
busy lately to do this. I'd like to get to it soon though (i.e. this year
;o)
As for AMBER-99SB, the paper makes reasonable arguments I think, but I've
not run any real test or production runs with 99SB myself, so I can't
comment on it w.r.t. any specific systems.
Eric
----- Original Message -----
From: "Maik Goette" <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>;
<[EMAIL PROTECTED]>
Sent: Friday, September 28, 2007 2:57 AM
Subject: Re: [gmx-users] ffamber updates
Hi Eric
Thanks for doing that great job concerning the amberFF for GROMACS.
I recently came across this paper:
http://www.biophysj.org/cgi/content/abstract/92/11/3817?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1&FIRSTINDEX=0&volume=92&firstpage=3817&resourcetype=HWCIT
There Perez et al refined new alpha/gamma angles for nucleic acids. They
claim, that these dihedrals in the original amber99 lead to irreversible
transitions, which have an influence on the correct conformation of
NA-strands.
I thought about including them in the amber99-GROMACS port, but maybe it's
better if you do, because you have more experience in building the
amber-ports. What do you think?
I didn't read the paper according to your 99sb-port yet. Do you think it
makes sense to switch from the amber99 to amber99sb?
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Eric J. Sorin wrote:
Hi GROMACS users,
We've updated our ffamber ports to include the AMBER-99SB force field.
Please visit the new website for information and downloads:
http://chemistry.csulb.edu/ffamber/.
Eric _______________________________________________
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