On Tue, Apr 7, 2015 at 1:17 AM, Swithin Hanosh <swithinhanosh.gmail.com>
wrote:
> Dear Amber users,
>
> I am following the antechamber tutorial 4b for creating topology and
> co-ordinate
> files for a complex. After creating .prmtop and .inpcrd file for the
> organic molecule using R.E.D server created .mol2 file, I tried to complex
> the organic molecule with the protein. But, it was showing the error that
> the molecule is an unknown residue and atoms were not in its residue
> template. An archive file of the operation is attached with the mail.
>
> The commands typed are :
>
> 1. parmchk -i sam.mol2 -f mol2 -o sam.frcmod
> 2. tleap -f leaprc.ff12SB
> 3. source leaprc.gaff
> 4. dem = loadmol2 sam.mol2
>
This command right here loads the molecule in "sam.mol2" and assigns it
the name dem, which is probably not right. You need to assign it the name
that it has in the PDB file (and it should be uppercase, since case
matters). Check your error message, the unrecognized residue should be
printed to the screen in the error message -- that's what you should be
naming sam.mol2.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 07 2015 - 05:30:02 PDT
