Sir,
on sourcing leaprc.ff99bsc0 , parameters of aminoacids are also seems to
be loading.
Then should i load again by
source leaprc.ff99SB.
Does sourcing leaprc.ff99bsc0 takes care of both nucleic acid and dipeptide.
Also on loading into leap the his-his dipeptide the second His residue gets
added OXT atom with the C=O bond. is it correct.?
Thanking you
On Tue, Sep 4, 2012 at 3:25 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Mary,
>
> > I have to do a simulation study on nucleic acid-dipeptide complex. Can i
> > use a combination ff99bsc0 and ff99SB. I thought as i am using standard
> > aminoacid dipeptide as the ligand i dont have to do any QM charge
> > derivation procedure. ff99SB would take care of it. Am Icorrect?
>
> ff99SB and ff99bsc0 handle regular amino-acid and nucleic acid residues.
> A regular aminoacid dipeptide should be handled by ff99SB...
>
> regards, Francois
>
>
>
>
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--
Mary Varughese
Research Scholar
School of Pure and Applied Physics
Mahatma Gandhi University
India
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Received on Fri Sep 07 2012 - 10:00:03 PDT
