From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Feb 15 2010 - 03:46:29 CST
Please disregard my previous thread of similar name. Just to restart
from a clean basis.
I prepared with VMD 1.8.7 psf and pdb files for a system containing
heme (thus, top_all27_prot_lipid_na.inp and
par_all27_prot_lipid_na.inp). Solvated and neutralized.
NAMD2.7b2 complains that parameters for C - CPB bond are lacking.
I checked the structure of my molecule, heme is OK.
I checked the top file: bond C - CPB present.
I also checked the par file: no C - CPB, as namd complainsed, while
parameters for bonds C-CT3, C-CT2, C-CT1, C-CP1, C-C, C-N, C-NC2,
C-NH1, C-O are present)
As far as I understand, parameters for C-CPB bond (CAB-C3B in atom
names, for the bond between a vinyl group and a pyrrole ring) are
Much indebted for suggestions how to remedy.
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