From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Feb 15 2010 - 08:15:53 CST
Googling "heme cpb bond parameter missing" led me to this: http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=8414&site_id=1#import
I'll need to fix the heme topology in the files bundled with VMD. However, this does raise an important point: one should not totally rely on the files distributed in VMD as they are not meant to have complete coverage of the forcefield. It's always best to get the full set of topology and parameters from MacKerell's website.
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Francesco Pietra
Sent: Monday, February 15, 2010 3:46 AM
To: vmd; NAMD
Subject: namd-l: Can't find C-PDB bond parameters
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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