Many thanks Dave. Yes, Shirts paper from 2003 was the first to do this and
then some other people also followed the same procedure. I did check those
papers but didn't find anything in more detail than this. But it is clear
enough and it should be possible by creating and editing lib/off files for
each residue.
I just thought to check if such files are already available somewhere as
GROMOS probably has something like that (I am not sure though!).
Best,
Mish
On Thu, Jan 31, 2019 at 12:46 PM David A Case <david.case.rutgers.edu>
wrote:
> On Thu, Jan 31, 2019, mish wrote:
>
> >I thought it makes sense to
> >keep the side-chain part exactly same as in AMBER14 force-field and just
> to
> >change it on Cb. This is going to affect some properties but the
> >interaction of side-chain part with my small molecules may not be affected
> >much and I can still keep parameters closer to native AMBER force-field.
>
> I agree with the above. Among other things, there are lots of
> calculations out there that have used exactly this scheme. (I think
> Michael Shirts was the first to do this, but I'm not sure.) Certainly,
> if you plan to draw some conclusions about the Amber14SB force field,
> this seems like the best way to proceed. (At least to me.) Since there
> are only 19 amino acid sidechains, it wouldn't take very long to just do
> it.
>
> OR, check the supplementary materials in the literature. People that
> have carried out these sorts of calculations are quite diligent in
> providing complete details of what they have done. So there might be
> some files out there. The relevent authors are probably not following
> the Amber mailing list. Try an email to Michael or David Mobely.
>
> ...good luck...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 31 2019 - 05:30:02 PST
