You are right. I loaded the gaff leaprc file. I just used leaprc.ff12SB and
the problem is solved. My commands:
In terminal: xleap
In xleap: source leaprc.ff12SB
x=loadpdb xxx.pdb
And xleap added all missing atoms. Thanks for your helps.
2015-02-05 21:46 GMT+01:00 Jason Swails <jason.swails.gmail.com>:
>
> > 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Ahmet Yıldırım
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 05 2015 - 13:00:05 PST
