[AMBER] CHAMBER: error in finding bond type

From: Mike Limb <mikeallimb.gmail.com>
Date: Tue, 16 Oct 2012 12:28:26 +0100

Dear Amber users,

I am currently trying to use CHAMBER in order to convert my CHARMM
compatible files to use in AMBER.

My system contains is solvated with explicit solvent and contains a signal
chain enzyme and a ligand (for which I have custom developed CHARMM

I use the command:

chamber -cmap -top nag_nam_protein_top_CMAP.inp -param
par_sugar_protein_chamber.inp -psf hewl_mgm1_solv_charmm.psf -crd
ionized.pdb -p hewl_sugar.prmtop -inpcrd hewl_sugar.inpcrd

produces error:

          PSF input parsing summary

                        Number of PSF flags found: 3

                            Number of atoms found: 22839
                         Number of residues found: 7064

                            Number of bonds found: 22848
                           Number of angles found: 10654
                        Number of dihedrals found: 5458
                        Number of impropers found: 361

                           Number of donors found: 281
                        Number of acceptors found: 7125
    Number of explicit nonbonded exclusions found: 0

                           Number of groups found: 7533
                       Number of ST2 waters found: 0

                      Number of cross terms found: 127

 Trouble in river city, nt /= nattypes
   --- Found all ATOM TYPES in topology file

   --- Found all nonbond parameters
 <bond_types>error in finding bond type 1990 0 0
 Cannot continue

Investigating 1990 I found it to be an atom O9 in my ligand which makes
only one bond with atom no. 1988
on checking (as far as I can see....) in the parameter file, psf and
topology has all the correct bond definitions
                                          bond: 1988 - 1990
                               name in pdb: C10 - O9

> atom type: CC (32) - OC (72)

I am a first time AMBER user so any help or pointers of how to solve this
problem would be gratefully welcomed!

Thanks in advance,

Mike Limb

Centre for Computational Chemistry
Prof. Adrian Mulholland
School of Chemistry
University of Bristol
Bristol BS8 1TS http://www.chm.bris.ac.uk/pt/ajm/Site/Home.html
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Received on Tue Oct 16 2012 - 04:30:03 PDT
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