Re: [AMBER] problem converting AmbertoDesmond

From: Albert <>
Date: Mon, 16 Apr 2012 23:15:15 +0200

thank you very much for reply.
problem solved with the latest Schrodinger2012 suite.....


On 04/16/2012 09:30 PM, David A Case wrote:
> 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.
> ....dac
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Received on Mon Apr 16 2012 - 14:30:02 PDT
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