On Wed, Apr 29, 2015 at 2:15 PM, Francesco Gentile <fgentile.ualberta.ca>
wrote:
> Hello,
> I am trying to do mmpbsa analysis on calcite surface. I used antechamber to
> parametrize the surface and as it couldn't recognize the calcium ion I used
> xleap to create the library for calcium and I could create the prmtop for
> the surface. and in the prmtop the calcium was recognised.
> these are the parameter I used for calcium:
>
> residue name: Ca2
> atom name: Ca1 (as default in xleap)
> atom type : C0
> charge : +2
> element: Ca
>
> but when I was using this prmtop for mmpbsa it couldn't recognize the
> calcium and it was treating it as carbon alpha. so giving me the error "
> bad number of bond to C".
> I was wondering if anyone has any suggestion?
>
​What version of Amber are you using? Newer versions should be using the
atomic number stored in the prmtop file rather than the atom name or type
name (so there really should not be any chance of it interpreting calcium
ions as carbon atoms.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 30 2015 - 10:00:03 PDT
