[gmx-users] Nucleic Acid Simulations with Gromacs

[Monika Sharma]

Thank you all for helping me. I will surely try the ffamber ports 
available.
Regards,
monika


Yang Ye wrote:
> 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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