From: JIMENEZ Ralph (rjimenez_at_jilau1.Colorado.EDU)
Date: Wed Oct 05 2005 - 14:54:26 CDT
Hi everyone.
I'm attempting to build the psf file for a heme containing protein, but
it generates a heme conformation with the pyrrole nitrogens in a
tetrahedral geometry around the Fe atom, rather than nearly in the plane
with the rest of the ring. My input file for VMD (to generate the PSF)
looks like this:
package require psfgen
topology
/usr/local/lib/vmd-1.8.3/plugins/noarch/tcl/membrane1.0/top_all27_prot_lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
alias residue HEM HEME
segment U {pdb 1drm_trunc_mainchain.pdb}
segment H {pdb 1drm_trunc_heme.pdb}
coordpdb 1drm_trunc_mainchain.pdb U
coordpdb 1drm_trunc_heme.pdb H
guesscoord
writepdb 1drm_holo_withH.pdb
writepsf 1drm_holo_withH.psf
and it generates a few errors (I've included only the heme-related errors):
Warning: poorly guessed coordinate for atom NA HEME:719 H
Warning: poorly guessed coordinate for atom NB HEME:719 H
Warning: poorly guessed coordinate for atom NC HEME:719 H
Warning: poorly guessed coordinate for atom ND HEME:719 H
Warning: poorly guessed coordinate for atom HA HEME:719 H
Warning: poorly guessed coordinate for atom HB HEME:719 H
Warning: poorly guessed coordinate for atom HC HEME:719 H
Warning: poorly guessed coordinate for atom HD HEME:719 H
Warning: poorly guessed coordinate for atom HMA1 HEME:719 H
Warning: poorly guessed coordinate for atom HMA2 HEME:719 H
Warning: poorly guessed coordinate for atom HMA3 HEME:719 H
Warning: poorly guessed coordinate for atom HAA1 HEME:719 H
Warning: poorly guessed coordinate for atom HAA2 HEME:719 H
Warning: poorly guessed coordinate for atom HBA1 HEME:719 H
Warning: poorly guessed coordinate for atom HBA2 HEME:719 H
Warning: poorly guessed coordinate for atom HMB1 HEME:719 H
Warning: poorly guessed coordinate for atom HMB2 HEME:719 H
Warning: poorly guessed coordinate for atom HMB3 HEME:719 H
Warning: poorly guessed coordinate for atom HAB HEME:719 H
Warning: poorly guessed coordinate for atom HBB1 HEME:719 H
Warning: poorly guessed coordinate for atom HBB2 HEME:719 H
Warning: poorly guessed coordinate for atom HMC1 HEME:719 H
Warning: poorly guessed coordinate for atom HMC2 HEME:719 H
Warning: poorly guessed coordinate for atom HMC3 HEME:719 H
Warning: poorly guessed coordinate for atom HAC HEME:719 H
Warning: poorly guessed coordinate for atom HBC1 HEME:719 H
Warning: poorly guessed coordinate for atom HBC2 HEME:719 H
Warning: poorly guessed coordinate for atom HMD1 HEME:719 H
Warning: poorly guessed coordinate for atom HMD2 HEME:719 H
Warning: poorly guessed coordinate for atom HMD3 HEME:719 H
Warning: poorly guessed coordinate for atom HAD1 HEME:719 H
Warning: poorly guessed coordinate for atom HAD2 HEME:719 H
Warning: poorly guessed coordinate for atom HBD1 HEME:719 H
Warning: poorly guessed coordinate for atom HBD2 HEME:719 H
I checked top_all27_prot_lipid.inp for a heme entry, and it definitely has
one, although it's for "RESI HEME -2.00 ! 6-liganded planar heme"
In my system, the Fe should be 5-coordinate (4 N's from the ring, and one
histidine from the protein). Should I be using a parameter file with a
5-coordinate heme entry?
Does anyone have a suggestion? Shouldn't I expect a "normal" looking heme?
Thank you for suggestions and tips...
Ralph
JILA/NIST and Dept. of Chemistry & Biochemistry
University of Colorado, Boulder
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