Re: [AMBER] ligand topology genaration

From: Jason Swails <>
Date: Tue, 5 Jan 2016 07:38:52 -0500

On Tue, Jan 5, 2016 at 5:24 AM, neha chaudhary <>

> Hello Sir/Ma'am,
> 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
> Could not find bond parameter for: C - H

​It is missing a lot of parameters (and these appear to be Amber atom
types, not GAFF atom types). Is this intentional? Did you forget to load
either (or both) the frcmod file and original force field you derived
parameters from?

​These error messages suggest to me that you made a mistake somewhere​.
The general process you outlined (use antechamber and parmchk to generate a
mol2 and frcmod file for a ligand residue) is "correct" (although not at
all detailed), so there must be a difference between what you did and what
is outlined in the instructional ligand-parametrization tutorials at However, you haven't given us enough
information to even guess at what that might be.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Jan 05 2016 - 05:00:04 PST
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