AMBER Archive (2009)

Subject: Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?

From: Marek Malý (maly_at_sci.ujep.cz)
Date: Tue Apr 14 2009 - 19:40:22 CDT

Dear Ross,

thanks again ! I have just last technical question here.

You mentioned "dihedral barriers". I am not an expert here but
I think that you mean potential energy barriers which
prevents parts of molecules rotate freely around given bonds.

I am very curious here (regarding to my another actual problem with
finding of proper dihedrals for C-Si-C-C, C-Si-O-C for AMBER calculation)
is there
any tool in AMBER 10 package which can be used for evaluation of
rotational energy
profiles ? (with respect to choosen "rotation" bond).

Best wishes,

   Marek

Dne Wed, 15 Apr 2009 01:27:37 +0200 Ross Walker <ross_at_rosswalker.co.uk>
napsal/-a:

> Hi Marek,
>
>> thank you very much for your complex and valuable answer !
>>
>> Just for the curiosity, is this discussed combination:
>>
>> GLYCAM_06 + ff99SB + GAFF
>>
>> remarkably better solution than only:
>>
>> ff99SB + GAFF
>>
>> ?
>
> I would be VERY surprised if GAFF gets the subtleties of conformation in
> sugars correct. To the point that I think the error would be larger than
> the
> 1-4 scaling not necessarily being optimal. This is only a hunch though, I
> have not tried it. Your best option would probably be to try a single
> maltose and let Antechamber parameterise it and then compare certain
> properties (dihedral barriers etc) with the Glycam 06 ones. This will
> give
> you an idea of the differences.
>
> Rob Woods can probably comment some more on this.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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