> On Feb 5, 2015, at 2:47 PM, Ahmet yıldırım <ahmedo047.gmail.com> wrote:
>
> OK. I wont use the File menu :) I just used the commands in xleap but this
> time i got a different problem.
> I typed "xleap" on terminal. And then in xleap i typed: x=loadpdb xxx.pdb
> Screen ouput:
>
> Loading PDB file: ./xxx.pdb
> Unknown residue: ARG number=0
> .....
> total atoms in file:1424
>
> Whereas there are a few missing atoms in pdb file. But xleap didn't add
> them. Why?
It looks like you just loaded the gaff leaprc file, is this correct? leaprc.gaff does not define any of the standard amino acid or nucleic acid residues. You *also* need to source the leaprc of the Amber FF you want to use (e.g., leaprc.ff14SB).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 05 2015 - 13:00:03 PST
