Re: Changing the protonation states of residues

From: Gaurav Sharma (sharma_at_coe.neu.edu)
Date: Tue Mar 06 2007 - 18:08:04 CST

Nabajyoti:

These warnings are common with most psfgen runs so you can ignore them.
The easiest way to check if your residues are protonated is to calculate
the intial and final charge on your system before and after protonation.
The total charge after protonation should be higher. The autoionize
plugin actually gives the initial charge on your system before placing
ions to neutralize it. So you can run the autoionize plugin on your
unprotonated and protonated system to compare the charges.

Hope this helps.

Gaurav

Nabajyoti Goswami wrote:

> 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 <http://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

-- 
Gaurav Sharma
Computational BioNano Robotics Lab
Northeastern University
Boston, MA - 02115
Tel: 617-373-2970
http://www.bionano.neu.edu/ 

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