VMD-L Mailing List

From: Allen, Caley R (caley.allen_at_chemistry.gatech.edu)
Date: Mon Jan 27 2014 - 12:32:45 CST

Hello Tristan,

Thank you for sharing the link with me. The Glu is unstructured, so a simple deletion of the residue may work. However, I also found in the pdb that there is an Ala residue reported to be missing from the N-terminus. So I may just simply add that residue back and solve the issue.

I appreciate your advice!

Again thank you.
Best,
Caley

----- Original Message -----
From: "Tristan Croll" <tristan.croll_at_qut.edu.au>
To: "Caley R Allen" <caley.allen_at_chemistry.gatech.edu>, vmd-l_at_ks.uiuc.edu
Sent: Friday, January 24, 2014 3:49:22 AM
Subject: RE: vmd-l: FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR NH3 CT1 CT2A CT2 (ATOMS 1 5 7 10)

Hi Caley,

I ran into this problem a while back, and received help on the namd-l list. See http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2012-2013/3273.html.

Cheers,

Tristan

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Allen, Caley R
Sent: Friday, 24 January 2014 5:37 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR NH3 CT1 CT2A CT2 (ATOMS 1 5 7 10)

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)