AMBER Archive (2009)

Subject: Re: [AMBER] antechamber

From: Alan (alanwilter_at_gmail.com)
Date: Thu Jul 02 2009 - 05:16:55 CDT

I second François here.
However I have another way too. Look at acpypi.googlecode.com and read it
well to understand what's written below.

- With pymol, relax your t80p.pdb file.
  cmd.sculpt_activate('t80p')
   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
charges.
- 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 amb2gmx.pl, instead of
using amb2gmx.pl, 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.
Alan

On Thu, Jul 2, 2009 at 07:33, FyD <fyd_at_q4md-forcefieldtools.org> 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 amb2gmx.pl. 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 @
> http://q4md-forcefieldtools.org/Tutorial/
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
>
> 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
>
>
>
> _______________________________________________
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> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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