[gmx-users] ffamber updates

[Eric J. Sorin]

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" <mgoette at mpi-bpc.mpg.de>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>; 
<esorin at csulb.edu>
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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