[gmx-users] Nucleic Acid Simulations with Gromacs

[Yang Ye]

Please don't use the OPLS NA forcefield. It is largely based on AMBER 
(OPLS takes different approach in parameterization, so you know that 
direct migration is so correct) and not verified. I had some 
communications with that group on this issue. It has some teaching value 
on making topology of small molecules in OPLS format but except this, 
don't use for serious business.

Regards,
Yang Ye

On 10/2/2007 6:58 PM, gigo at poczta.ibb.waw.pl wrote:
> Hi,
> On the gromacs webpage in user contributions->topologies you have (at 
> least) 2 forcefields do download that allow you to simulate NA. The 
> first is OPLS NA records from rnp-group
> (http://rnp-group.genebee.msu.su/3d/oplsa_ff.html). It is for gromacs 
> 3.2.1, so minor manual adjustments for 3.3.1 are required. The second 
> is AMBER ff variants from Stanford 
> (http://folding.stanford.edu/ffamber/).
> Good Luck
>
>
> Grzegorz Wieczorek
> Department of Bioinformatics
> Institute of Biochemistry and Biophysics
> Polish Academy of Sciences
> ul. Pawinskiego 5a
> 02-106 Warszawa, Poland
>
> On Tue, 2 Oct 2007, Monika Sharma wrote:
>
>> Dear All,
>> I want to start nucleic acid simulations. I am using gromacs3.3.1. 
>> But I could not find any mention of Nucleic Acids in any of the 
>> force-field provided by gromacs distro. So does it mean that one _can 
>> not_ simulate nucleic acids with gromacs. Has anyone tried? And if 
>> someone can guide me through??
>> Thanks in advance
>> Regards,
>> Monika
>>
>>
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