Hi,
For ligand, i first used antechamber as
>antechamber -i ligand.mol2 -fi mol2 -o ligand.prep -fo prepi
>parmchk -i ligand.prep -f prepi -o ligand.frcmod
>tleap
>source leaprc.gaff
>loadAmberParams ligand.frcmod
>LIG = loadMol2 ligand.mol2
>saveAmberParm LIG ligand.top ligand.crd
ligand topology files generated without error.
For protein:
>tleap
>source leaprc.gaff
>receptor = loadPDB protein.pdb
Then error message came. I am attaching the error file herewith.
I am not getting how to assign atomtype to amino acid residues for the
protein.
Best Regards,
*Neha*
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,
On Thu, Jan 7, 2016 at 5:22 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Jan 7, 2016 at 12:33 AM, neha chaudhary <
> nehachaudhary769.gmail.com>
> wrote:
>
> > Hi,
> >
> > Thanks for replying. I have done MD simulations of protein-ligand complex
> > in Gromacs earlier now I want to convert the output files into Amber
> > format. I am trying to generate .prmtop files for protein, ligand and
> > protein-ligand complex. I am attaching input pdb files of protein, ligand
> > and protein-ligand complex herewith.
> >
>
> We still need to know the exact commands you were using, as well as the
> exact error messages you were receiving when trying those commands.
> Otherwise we have to guess, which is more often than not a waste of time.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Jan 07 2016 - 04:30:03 PST
