AMBER Archive (2009)

Subject: Re: [AMBER] antechamber

From: Alan (
Date: Thu Jul 02 2009 - 05:16:55 CDT

I second Fran├žois here.
However I have another way too. Look at and read it
well to understand what's written below.

- With pymol, relax your t80p.pdb file.
   for n in range(100): cmd.sculpt_iterate('t80p')
- Ideally you should define a selecting conformation for your molecule as
FyD asked.
- then since, 'acpypi -di t80p.pdb' will fail because of mopac (you may want
to look at mopac.out to know why and try to solve it).
- you could use 'acpypi -di t80p.pdb -c gas'. This will at least generate
the topology with Gasteiger method for charges, although not the best set of
- Another way to get better charges would be to use QM/Semi-empirical
methods (see RED from FyD). If you have these charges for your molecule in a
MOL2 format, than you could do this:
'acpypi -di t80p.mol2 -c user' and you'd get the topology with charges
(previously calculated by other program).
- and since it seems that you want to use Leap to generate the inpcrd and
prmtop files and then convert them to gromacs with, instead of
using, you could do:
'acpypi -x complex.inpcrd -p complex.prmtop'
and then you'd have the files ready for Gromacs. Or use the topologies files
generated by acpypi for your t80p (something like t80p_GMX.itp) and use
Gromacs pdb2gmx etc. to build your system in Gromacs (see acpypi's wikis).

Good luck.

On Thu, Jul 2, 2009 at 07:33, FyD <> wrote:

> Dear RAK,
> Thank you so much for your kind reply...I ll check it out again. Just I m
>> preparing topology for gromacs using if I cut my structure
>> into two part and run antechamber, there wont be any problem in
>> combining the two topology together later using this script? if so how I
>> should do that. any tutorial for such a thing?
> Usually, cutting a structure in 2 is not enough. You need:
> - to find the chemical group where you are going to cut your structure in
> 2.
> - to define connecting groups where you cut your structure.
> Thus, this is not cutting a molecule in 2 parts, but more cutting a
> molecule in 2 molecules from which some atoms have to be removed.
> You can get many information about such an approach @
> Finally, after looking at your PDB file, all the hydrogens are located at
> the end of the file. You might be interested in using Ante_R.E.D. which
> reorders atoms so that hydrogens are always located after the heavy atom
> they are bound to.
> regards, Francois
> _______________________________________________
> AMBER mailing list

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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