Re: [AMBER] ligand topology genaration

From: David A Case <>
Date: Tue, 5 Jan 2016 08:20:39 -0500

On Tue, Jan 05, 2016, neha chaudhary wrote:
> I want to generate ligand topology files ( and lig.crd) for my
> ligand. For this, first I generated .prep and .frcmod files using
> antechamber and parmchk respectively without any error. Further, I am
> trying to generate topology for the same molecule with tleap, but I am
> getting the following errors. I am attaching the error herewith, please
> help to solve the problem:
> >saveAmberParm LIG cel.crd
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: C - S
> Could not find bond parameter for: C - H


Two things come to mind:

1. You didn't tell us anything about what parameter files or leaprc files you
loaded. Generally, for a ligand, you would have to load leaprc.gaff.

2. You atom types are upper case, indicating that these are Amber atom types,
not gaff atom types. Again, I have to guess a lot, since you said very little
in your email about what you actually did. But you probably want to avoid
anything like "-at amber" at the antechamber step: make sure your atom types
in the output mol2 (or off) file are lower case.

...hope this helps....dac

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Received on Tue Jan 05 2016 - 05:30:04 PST
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