Re: [AMBER] problem converting AmbertoDesmond

From: David A Case <>
Date: Mon, 16 Apr 2012 15:30:49 -0400

On Mon, Apr 16, 2012, Albert wrote:

> I am following the guide at : and
> trying to convert an Amber MD system into Desmond system. It do
> generated a .cms file, but what I found is that all the residues are
> renamed 'UNK' and we cannot differentiate which one is which one when I
> import to VMD or Maestro..

You should probably take these questions to the Schrodinger people, since they
are the ones who have written these codes. My experience is that they are
generally quite helpful.

The "UNK" behavior is what we see as well.

.. Moreover, I try to run 'build constrain steps', there are some problems:
> ValueError: No angle found for atoms 4684 4683 4685

All I can say here is that, according to what I have been told(!?!), this step
is not needed. I'm guessing that atoms 4683 to 4685 form a water molecule,
and Amber typically does not keep the force constants for those. Given LEaP
the command "set default flexible water on" before making the Amber prmtop
may help.


AMBER mailing list
Received on Mon Apr 16 2012 - 13:00:02 PDT
Custom Search