From: Thomas Freeman (Thomas.L.Freeman_at_dartmouth.edu)
Date: Mon Feb 28 2011 - 13:46:04 CST
I am currently trying to generate a pdb and psf file for a protein with
a c-type heme but have been getting a number of errors shown below. I am
using the topology file for cytochrome c from: Journal of Computational
Chemistry, 25, 1613-1622 (2004).
..
Warning: failed to set coordinate for atom O GLU:161 PROT
..
Warning: poorly guessed coordinates for 13 atoms (2 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1 SER:36 PROT
Warning: poorly guessed coordinate for atom HT2 SER:36 PROT
Warning: poorly guessed coordinate for atom HT3 SER:36 PROT
Warning: poorly guessed coordinate for atom HG2 PRO:98 PROT
Warning: poorly guessed coordinate for atom HG2 PRO:102 PROT
Warning: poorly guessed coordinate for atom HG2 PRO:135 PROT
Warning: poorly guessed coordinate for atom OT1 GLU:161 PROT
Warning: poorly guessed coordinate for atom OT2 GLU:161 PROT
Warning: poorly guessed coordinate for atom HA HEMO:199 HEC
Warning: poorly guessed coordinate for atom HB HEMO:199 HEC
Warning: poorly guessed coordinate for atom HC HEMO:199 HEC
Warning: poorly guessed coordinate for atom HD HEMO:199 HEC
Warning: poorly guessed coordinate for atom HBD2 HEMO:199 HEC
Warning: failed to guess coordinates for 1 atoms
The psfgen input file I am using is:
kdir -p output
package require psfgen
# Load topology files
topology toppar/top_c_heme.inp
topology toppar/top_all22_prot.inp
# Generate protein segment
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment PROT {pdb 3b42-chainA-plain.pdb}
coordpdb 3b42-chainA-plain.pdb PROT
# Create segment for heme group
# Prevent NTER and CTER patches
pdbalias residue HEM HEMO
segment HEC {
first none
last none
pdb 3b42-chainA-heme-plain.pdb
}
coordpdb 3b42-chainA-heme-plain.pdb HEC
# Bind heme to protein using HOCY patch
patch HOCY PROT:140 PROT:143 PROT:144 PROT:60 HEC:199
guesscoord
# Create output files
writepdb output/3b42-chainA-psf-output.pdb
writepsf output/3b42-chainA-psf-output.psf
Opening up the pdb file that was generated shows a hydrogen atom (His
144 HD1) that is disconnected from the protein chain by at least 10
angstroms.
Any ideas for why this might be occurring and why the HD1 hydrogen
coordinates are so different from what they should be and not generating
any sort of error?
Thanks,
-- Thomas Freeman Graduate Student Pletneva Research Group Department of Chemistry Dartmouth College
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