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
parameters).
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
1
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
*ml7684*.bristol.ac.uk<Adrian.Mulholland.bristol.ac.uk>
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
