From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Jan 23 2014 - 15:12:34 CST

Hi Caley,

In all likelihood you did nothing wrong, but ran into a shortcoming of
the force field. When you generated the psf/pdb pair, since glutamate
was the first residue in the chain, psfgen thinks it needs to apply a
patch there to make it the N-terminus. This changes (among other things)
the backbone nitrogen from type NH1 to NH3, and there aren't parameters
in the force field to account for that.

There are a few things you can try. Many crystal structures are reported
as truncated forms of the full-length protein, since they are floppy and
not resolved well. Adding in those missing residues on the front and
back may mean that a glutamate is no longer the leading residue, and
this problem goes away. Supposing the only missing residue was an
alanine at residue 1 of chain H, this is what you'd change the segment
declaration to (see the psfgen user guide for more details):

segment U {
        residue 1 ALA H
        pdb H.pdb
        auto angles dihedrals
}

Another possible solution is just to assume that the dihedral potential
didn't change upon changing to an N-terminus. What you would do then is
look for the dihedral parameter listing with NH1 instead of NH3. In
par_all36_prot.prm, the lines are:
CT2 CT2A CT1 NH1 0.3000 1 0.00
CT2 CT2A CT1 NH1 0.3500 2 0.00
CT2 CT2A CT1 NH1 1.7600 3 0.00
You would add these a second time with a NH1 replaced by NH3. I like to
put these in a separate file (extradihedrals.prm) to remind myself that
I was monkeying around with the force field, since NAMD has no effective
limit on the number of parameter files it can read in.

That being said, I'd check option 1 first, since adding terms to the
force field shouldn't generally be done without a good reason.

-Josh Vermaas

On 01/23/2014 01:37 PM, Allen, Caley R wrote:
> Greetings All,
>
> I have obtained a pdb file from pdb.org. After generating the psf/pdb combo using psfgen (script is below), adding a solvation box and ionizing the box in VMD- I attempt to equilibrate/minimize the protein + water + ions and I quickly get the following CHARMM error: "FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR NH3 CT1 CT2A CT2 (ATOMS 1 5 7 10)". The first residue, which the error is referring to is GLU. I have researched on this mailing list (where I found plenty about fatal errors relating to angles) and other resources and still can not seem to correct this issue. Any advice is appreciated. If more information is required please just let me know.
>
> Cheers,
> Caley
>
> psfgen script:
>
> package require psfgen
> topology top_all36_prot.rtf
> pdbalias residue HIS HSE
> pdbalias atom ILE QD1 CD
> segment U {
> pdb H.pdb
> auto angles dihedrals
> }
> coordpdb H.pdb U
> guesscoord
> writepdb H36.pdb
> writepsf H36.psf
>
>
> In output file:
>
> Reason: FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR NH3 CT1 CT2A CT2 (ATOMS 1 5 7 10)
>
> Charm++ fatal error:
> FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR NH3 CT1 CT2A CT2 (ATOMS 1 5 7 10)
>
>
>