On Fri, 2014-11-07 at 19:09 +0530, Ruchika Bhat wrote:
> ?Hi everyone,
>
> Please guide me what is the command to generate the top and crd file once I
> generated the frcmod and prepin files.
>
> In the command
> > saveamberparm DRG ligand.prmtop ligand.inpcrd
This one works?
> The DRG = loadpdb pdb1_10854218DOCK.pdb
>
> But when I load the DRG with the protein ligand complex it is giving:
>
>
> Loading PDB file: ./pdb1_10854218DOCK.pdb
> Unknown residue: DRG number: 212 type: Terminal/last
This means you haven't loaded the DRG residue template. That would be
your "prepin" file. Did you load that prep file before trying to load
the PDB file? You need to make sure the residue AND atom names are the
same in both the prepin and PDB files.
Also, you may find some of the tutorials (
http://ambermd.org/tutorials)
helpful -- particularly
http://ambermd.org/tutorials/basic/tutorial4b/
that describes how to set up custom residues.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Nov 07 2014 - 06:30:03 PST
