Re: [AMBER] Antechamber preparartion

From: David A Case <>
Date: Mon, 29 Oct 2012 10:18:55 -0400

On Mon, Oct 29, 2012, Алексей Раевский wrote:
> Q1. How to prepare a correct molecule of the inhibitor?
> Adding all hydrogenes - it is OK thanks to chemaxon and openbabel.

I don't understand the question. Antechamber will probably fail if the input
files are bad. The "acdoctor" program can be used to identify some common

> Q2. But what about the inital conformation (is it important or I can use
> plane structure?) and atom type assignation (for example in PO3 group I
> have to use O.co2 atom type, as it is mentioned in tripos mol2 manual or
> )?

You don't need a perfect initial conformation, since antechamber will minimize
it (in AM1) before estimating charges. But this is just a minimization, so
the final configuration is likely to be close to the initial one. Antechamber
does not have any automatic way of averaging parameters over multiple
conformations. The input atom types are ignored, so it doesn't matter what
they are.

> Q3. Does it make reliable convertion from pdb ro mol2 or it is better to
> make some changes by hands in mol2 and then import it?

Up to you.

> Q4. What degree of accuracy this soft can provide? And, especially, what
> about biological molecule (derivatives) like ATP, modified amino acids?
> As I know developed for charmm27 had some problem with it.

For common functional groups like ATP, people have hand-optimized parameters:
see the contibuted parameters database, linked from the Amber web site.
Phosphates are espcially difficult to model since they are highly charged and
have more than one possible protonation state. No current method provides
any guarantee about the degree of accuracy of the resulting parameters.

> Q5. As I'm working with amber forcefield bith in gromacs4.5.5 and amber11
> I'm using AM1 bcc flag. So what about the string, is it correct?
> antechamber -i lig.pdb -fi pdb -o lig.mol2 -fo mol2 -c bcc -s 2

This will provide GAFF estimates of paraemters.


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Received on Mon Oct 29 2012 - 07:30:07 PDT
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