On Sun, May 23, 2010, William Flak wrote:
> I have added an extrapoint to my ligand and calculated the
> charge. During leap step I got an the following error:
> total atoms in file: 4900Â Â Leap added 1 missing atom according to
> residue templates:
> This unknown element as I believe is returned to EP atom in my
> PDB file. But I defined and loaded EP before loading my PDB
> file. My commands were as following:source leaprc.ff99SBsource
> leaprc.gaffloadamberparams EP.frcmodMOL = loadpdb MOL.pdb
This won't work. You can't just add an EP to the pdb file: atoms in the PDB
file must exactly match atoms in the residue library you load, and ff99SB
doesn't have any extra points.
Take a look at the libraries loaded by leaprc.GLYCAM_04EP or
leaprc.ff02polEP.r1. It is a *lot* of work to add extra points to the
description of ligands. Make sure you understand how things work in detail
for the extra point force fields already present, before trying to roll you
own.
....dac
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Received on Sun May 23 2010 - 16:00:03 PDT
