AMBER Archive (2008)

Subject: RE: AMBER: About antechamber and GAFF [UPDATED]

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Nov 26 2008 - 10:39:30 CST

Hi Stephane,

I'm not sure I completely understand what you have done here and what you
want to do. As I understand it you have a glycolipid that you have built a
prep or mol2 file for using antechamber and the GAFF force field. This
includes the charges, GAFF atom types and any missing parameters. However,
now you would like to use the Glycam06 force field instead for this
glycolipid is that correct?

Firstly it is possible to mix GAFF and Glycam06 - you can includes sugars
for example along with your GAFF lipid. There is a potential issue with the
nonbond 1-4 scaling but as I understand it from Rob Woods this is minor.
However, if you wanted instead to actually build you glycolipid with the
Glycam force field the first thing I would check is if this residue is
already included in the Glycam parameter set. If it isn't then you can
attempt to assign atom types by analogy. You could do this by loading your
antechamber generated mol2 or prep file into xleap, editing the unit,
selecting it completely in the edit window and then choosing edit selected
atoms. This will bring up a table where you can change the atom types from
gaff atom types (lower case) to the equivalent Glycam atom types. I suppose
that you could keep the AM1-BCC charges from antechamber although you should
probably lookup how the charges in the Glycam force field were derived to
see if this assumption is reasonable.

Then you can save a mol2 / prep / off file etc and load it in with your pdb
of a complete structure etc. You may also need to provide any missing bonds,
angles and dihedrals for combinations of glycam atom types that you used
that are not in the Glycam force field definitions.

Good luck
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Stephane Abel
> Sent: Wednesday, November 26, 2008 3:22 AM
> To: amber_at_scripps.edu
> Subject: AMBER: About antechamber and GAFF [UPDATED]
>
> My last message was not very clear,
>
>
> Below the correct message
>
>
> Hi AMBER users
>
>
> I have two little questions about GAFF and Antechamber. Last week I asked
> a
> question about simulations with glycolipid with AMBER force field
> (Glycam06 in this case). I received a response of David A Case and Mattew
> Tessier. They
> said me that a good starting point for using AMBER force field and
> obtain the partial charge of the molecule is to use Antechamber. So I have
> installed
> Ambertools without any problems and started the tutorials, especially
> the example B4 of Ross Walker. If understand well, Antechamber use Gaff
> for the assignation of the parameters of the molecule. I try with GAFF,
> and indeed i obtained the partial charges, for my molecule. Here come my
> questions, it is
> possible to change this force field and use Glycam06 ? Because I want to
> use only Glycam for my MD If yes, how I can
> do it ?
>
>
> Thank in advance for your help
>
>
> stefane
>
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