Re: [AMBER] A possible bug in t leap when creating topology file ?

From: David A Case <>
Date: Thu, 25 Jun 2015 08:22:39 -0400

On Wed, Jun 24, 2015, Arun Srikanth wrote:
> I am attaching the pdb file of the molecule I am working with (1mol.pdb
> file contains one molecule, 2mol.pdb contains 2 molecules).
> I need to get the amber topology file for 2mol.pdb

We would certainly need to know the exact commands you gave to tleap to create
the topology files.

> I generated amber topology file for a mixture of two molecules in two
> ways.
> First:
> Create a pdb file of two molecules using packmol which is 2mol.pdb. Get the
> topology file from amber.
> The number of dihedrals in this case is 205
> Second:
> With one mol2 file of the molecule use combine command in tleap to generate
> the topology file

Are the energies the same for the two cases? The "combine" command is *very*
rarely used by Amber developers, so there could be problem there, I suppose.
But we need more than just a qualitative description of what you did: we need
the exact commands that you used.


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Received on Thu Jun 25 2015 - 05:30:03 PDT
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