force fields are trained using a specific representation. there's no way to
expect that ff99SB (which was trained and tested without EP) could have EP
added without making it perform much, much worse. You could think about
adding EP and refitting everything, but be prepared to do all of the work
that was associated with ff99SB development- you won't be able to use those
parameters directly.
On Sun, May 23, 2010 at 6:53 PM, William Flak <williamflak.yahoo.com> wrote:
> 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 - 19:30:03 PDT
