Re: Changing the protonation states of residues

From: hl332_at_drexel.edu
Date: Tue Mar 06 2007 - 18:31:08 CST

ANother way to determine charge on any selection is this i guess:
Lets say for all atoms:
(Once pdb is loaded in vmd)

set sel [atomselect top "all"]
eval vecadd [$sel get charge]

Harish
 
-------------------------------------------------
Harish Vashisth (Ph.D Candidate)
CAT-361,Chemical & Biological Engg.
Drexel University, Philadelphia, PA
office: 215-895-5823

----- Original Message -----
From: Gaurav Sharma <sharma_at_coe.neu.edu>
Date: Tuesday, March 6, 2007 7:08 pm
Subject: Re: namd-l: Changing the protonation states of residues

> 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 <." target="l">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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