Re: [AMBER] Use of param.Frosst parameters to prepare a ligand in Ambertools?

From: David A Case <>
Date: Thu, 10 Aug 2017 13:47:54 -0400

On Wed, Aug 09, 2017, Anne Nierobisch wrote:
> I would like to use the "parm.frosst" parameters to prepare my ligands
> in Ambertools.

One would need to have a way to assign parm.frosst atom types to your ligand
(along with the am1-bcc atom types.) My understanding is that there are some
initial efforts along these lines, but nothing that is ready for any kind
of distribution.

The manual approach is to find ligands in the distribution that are close
to the one you have, and make a stab at assigning atom types for your
ligand. You can use antechamber to get AM1-BCC charges, and then manually
edit the mol2 file, changing the GAFF atom types to parm.frosst atom
types. Load this in conjunction with the parm.frosst frcmod file, into
tleap, and you can create a prmtop file!

Maybe others on the list will have more up-to-date info.


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Received on Thu Aug 10 2017 - 11:00:03 PDT
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