From: JIMENEZ Ralph (rjimenez_at_jilau1.Colorado.EDU)
Date: Thu Oct 06 2005 - 16:14:45 CDT
Hi everyone:
I'm getting an error when I start an NAMD run, having to do with the
5-coordinate heme cofactor in my system. The simulation works fine with
the solvated apo-protein. I built the heme protein using the topology
file top_all27_prot_lipid.inp and appears to look OK (in VMD) in a box of
water with a few counter-ions to neutralize the charge. The error I get
from NAMD is:
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN
PARAMETER FILES
Fatal error on PE 0> FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND C -
CPB IN PARAMETER FILES
Within the PSF for my system, here are the relevant lines:
1643 H 719 HEME C2A CPB -0.060000 12.0110 0
1644 H 719 HEME C3A CPB -0.060000 12.0110 0
1645 H 719 HEME C4A CPA 0.120000 12.0110 0
1646 H 719 HEME C1B CPA 0.120000 12.0110 0
1647 H 719 HEME C2B CPB -0.060000 12.0110 0
1648 H 719 HEME C3B CPB -0.060000 12.0110 0
1649 H 719 HEME C4B CPA 0.120000 12.0110 0
1650 H 719 HEME C1C CPA 0.120000 12.0110 0
1651 H 719 HEME C2C CPB -0.060000 12.0110 0
1652 H 719 HEME C3C CPB -0.060000 12.0110 0
1653 H 719 HEME C4C CPA 0.120000 12.0110 0
1654 H 719 HEME C1D CPA 0.120000 12.0110 0
1655 H 719 HEME C2D CPB -0.060000 12.0110 0
1656 H 719 HEME C3D CPB -0.060000 12.0110 0
the parameter file I'm using is par_all22_prot.inp which I checked, and it
does seem to have 6-coordinate heme entries.
Looks as if something is not named correctly...is there an
incompatibility between these topology and parameter files? Do I need to
rename or alias some atoms?
Thanks for your help.
Ralph
JILA/NIST and Dept. of Chemistry & Biochemistry
University of Colorado, Boulder
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