On Tue, Feb 26, 2019, Sasthi Charan Mandal wrote:
> I am trying to simulate protein-dna complex. I am preparing the
>system using ambertools 16. It is saying that for dna the recommended force
>field is bsc1 and for protein ff14SB. So for the protein-dna complex I can
>not find any suitable force field in ambertools tutorial. It would be very
>helpful if someone suggest any force field for the above system.
Can you say exactly where you are getting information about "recommended
force fields"? I looked through all the Amber Reference Manuals back to
2016, and all of them list leaprc.DNA.OL15 as the recommended DNA force
fields (see Table 3.1 or 3.2, depending on which version of the manual
you are looking at.)
If you have a protein-DNA complex, you would load both
leaprc.protein.ff14SB and leaprc.DNA.OL15 (and presumably a
leaprc.water.xxxx file as well) into tleap. See Note 2 at the very
beginning of Chap 3 for an example of a typical prolog to a tleap
session.
...hope this helps....dac
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Received on Tue Feb 26 2019 - 06:30:02 PST
