Dear Dr. CaseThanks for your fast reply. I did build up my ligand containing EP and loaded it before loading my PDB file. I am sorry for unsufficient information I supported. Here is my full commands:
source leaprc.gaffsource leaprc.ff99SBset default PBRadii mbondi2loadamberparams EP.frcmodLIG = loadmol2 LIG.mol2loadamberparams LIG.frcmodMOL = loadpdb MOL.pdb
Error: Leap added 1 missing atom
Do you mean, I couldn't use EP for my ligand with ff99SB forcefield? Yes, ff99SB doesn't have EP, but I identified it (loadamberparams EP.frcmod).
I read extra_pts.f file inside sander, I want just to include it as a point of charge, not treated as a normal atom (so noextra = 0 and this is the default); I don't need bond, angle and dihedral interactions to be involved in calculations (so frameon=1 as default). So, I am using the normal input file for my simulation.
I am reading more on simulation with EP, but there is no enough information about practical issues.Thanks for your help and sorry for any inconvenience caused.W. Flak
--- On Sun, 5/23/10, case <case.biomaps.rutgers.edu> wrote:
From: case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] EP with ff99SB
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Sunday, May 23, 2010, 10:32 PM
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 - 16:00:04 PDT
