Changing the protonation states of residues

From: Nabajyoti Goswami (nabajyoti.goswami_at_gmail.com)
Date: Mon Mar 05 2007 - 03:27:07 CST

Dear NAMD Users,

I am trying to generate psf and pdb file for a protein containing HEME.
Moreover I need to protonate HIS, ASP, GLU residues at the positions as I
have mentioned in the following psfgen script.

package require psfgen
topology top_all27_prot_lipid.inp
pdbalias residue HIS HSE
pdbalias residue HEM HEME
pdbalias atom ILE CD1 CD
segment U {pdb baglbnoHeme.pdb}
patch HSP U:26 U:62 U:64 U:71 U:98 U:100 U:115
patch ASPP U:17 U:28 U:35 U:36 U:94
patch GLUP U:4 U:9 U:13 U:39 U:60 U:61
patch GLUP U:75 U:82 U:89 U:103 U:107
segment H {pdb haem.pdb}
coordpdb baglbnoHeme.pdb U
coordpdb haem.pdb H
guesscoord
writepdb 2iis.pdb
writepsf 2iis.psf

The original pdb was 2IIS.pdb which contains heme and can be downloaded from
www.rcsb.org. I have splitted it into haem.pdb and baglbnoHeme.pdb by
removing heme from the original 2IIS.pdb and heme-less pdb is renamed as
baglbnoHeme.pdb.
Even when the residues are get protonated I am not sure that whether they
have been protonated correctly or not because of the following warnings:

Created by CHARMM version 27 1
aliasing residue HIS to HSE
aliasing residue HEM to HEME
aliasing residue ILE atom CD1 to CD
building segment U
reading residues from pdb file baglbnoHeme.pdb
extracted 119 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-HN at beginning of segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
U:1
U:119
Info: segment complete.
applying patch HSP to 7 residues
U:26 U:62 U:64 U:71 U:98 U:100 U:115
applying patch ASPP to 5 residues
U:17 U:28 U:35 U:36 U:94
applying patch GLUP to 6 residues
U:4 U:9 U:13 U:39 U:60 U:61
applying patch GLUP to 5 residues
U:75 U:82 U:89 U:103 U:107
building segment H
reading residues from pdb file haem.pdb
extracted 1 residues from pdb file
Info: generating structure...
Info: segment complete.
reading coordinates from pdb file baglbnoHeme.pdb for segment U
Warning: failed to set coordinate for atom O THR:119 U
Warning: failed to set coordinate for atom OXT THR:119 U
reading coordinates from pdb file haem.pdb for segment H
Info: guessing coordinates for 961 atoms (2 non-hydrogen)
Warning: poorly guessed coordinates for 49 atoms (2 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1 THR:1 U
Warning: poorly guessed coordinate for atom HT2 THR:1 U
Warning: poorly guessed coordinate for atom HT3 THR:1 U
Warning: poorly guessed coordinate for atom HE2 GLU:4 U
..so on.

So, if there is any help from any one will be appreciated .
thanks in advance..
Nabajyoti Goswami

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