AMBER Archive (2008)

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

From: Stephane Abel (Stephane.Abel_at_cea.fr)
Date: Thu Nov 27 2008 - 05:33:56 CST

Hi AMBER users

Firstly, i am a beginner with amber (Antechamber, leap, etc), indeed for
my previous simulations i use an other MD program with in the most case
the charmm force field.

Ross Walker wrote:

> 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.
Now What i did:

For the tutorial B4 I used a pdb file of one glycolipid molecule
obtained from a previous cpt simulation of a micelle (performed with the
CHARMM force field). I would like to compare these results with
simulations performed with the AMBER force field (and especially by
using GLYCAM06, which contains all the parameters for sugar and lipids).
Because no parameters exist in the literature for my glycolipid, I use
Antechamber to obtain the partial charges for the headgroup (maltose)
and alkyl tail (dodecane) . By following the tutorial I effectively
obtained the charges for the whole molecule.
> 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?
>
yes, and my (naive ?) question is: is it possible to use in Antechamber
GLYCAM06 force field instead GAFF to obtain the partial charge ? In
others words, the tutorial B4 can be done with GLYCAM06 instead GAFF,
by changing, for example, some parameters files in Antechamber.
> 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.
No maltose are include in Glycam06, only the glucose. Moreover I don't
want to mix GAFF and GLYCAM, but use only GLYCAM06 for the whole
molecule, since all the atoms of the molecule are include in this force
field.
> 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.
>
Here you partially answered my question. but I want to be sure. Can I
keep the charges obtained with GAFF and Antechamber if I use the
GLYCAM06 force field . Is the AM1-BCC are fully compatibles. If not how
to obtain the charges by an other approach (resp parameter in
Antechamber) and gaussian ?
> 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.
>
Thank you in advance for your help
> 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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>
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