AMBER Archive (2009)

Subject: Re: [AMBER] antechamber

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Jul 02 2009 - 01:33:46 CDT

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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