[gmx-users] about PRODRG

[Mark Abraham]

----- Original Message -----
From: fancy2012 <fancy2012 at yeah.net>
Date: Tuesday, May 25, 2010 18:43
Subject: [gmx-users] about PRODRG
To: gmx-users <gmx-users at gromacs.org>

> Dear GMX users,
>  When I prepare the topology file of one small molecule using PRODRG, I find that the generated topology file is for another molecule. The only difference between the two molecules is that the latter one has one more double bond. How should I deal with such problems? Thanks very much!

It's not possible to have such confusion with well-formed input. It sounds like you got the charge or number of atoms wrong, or mismatched some files.

Mark