Re: [AMBER] leap changes residue order

From: Hannes Loeffler <>
Date: Wed, 1 Jul 2015 17:12:05 +0100

On Wed, 1 Jul 2015 18:04:37 +0200
Ignacio Faustino <> wrote:

> Could you suggest me a way to keep the order of the residues from the
> input PDB? Or an alternative?

One possibility I see is to create a "custom" water molecule in a way
that leap would not recognise it. I guess renaming the residue should
do the trick but would also need a mol2/frcmod to reflect the original
parameters for your water type.

The other thing that comes to mind would be to look into ParmEd. I
guess some scripting with it to reorder molecules might work.


AMBER mailing list
Received on Wed Jul 01 2015 - 09:30:04 PDT
Custom Search