Re: [AMBER] Problem with amb2gmx in AmberTools 15

From: David A Case <>
Date: Tue, 19 May 2015 08:03:30 -0400

On Tue, May 19, 2015, Soumendranath Bhakat wrote:
> I am trying to convert an AMBER topology to to GROMACS using
> But I get this error during running. Can some one point out whats the
> problem in this case. Also amb2gmx seems to work fine with Amber 11 but as
> I generated PDB with TIP4Pew and FF14SB hence unfortumnately I will not
> able to reproduce the trajectory. Is there any way to fix this issue with
> amb2gmx in AmberTools15.
> | ambpdb (C++) Version V15.00
> Error: Option '-atm' is not yet supported.

You can compile the "old" version of ambpdb in this way:

   cd $AMBERHOME/AmberTools/src/etc
   make ambpdb

Then you would need to get this version of ambpdb to be first in you PATH,
or modify the script to use this version and not the one in

I'm not sure if this will work, since I've never used, but it
should remove the error listed above.


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Received on Tue May 19 2015 - 05:30:02 PDT
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