Hi,
Thanks for replying. Actually I want to prepare topology files for protein,
ligand and protein-ligand complex. I used leaprc.ff99SB parameter file
earlier. I tried with leaprc.gaff parameter files also but I am still
getting errors. Please help.
Best Regards,
*Neha*
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,
On Tue, Jan 5, 2016 at 6:50 PM, David A Case <david.case.rutgers.edu> wrote:
> On Tue, Jan 05, 2016, neha chaudhary wrote:
> >
> > I want to generate ligand topology files (lig.top 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.top 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 Wed Jan 06 2016 - 01:30:06 PST
