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, [EMAIL PROTECTED] 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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