Re: [gmx-users] Polar Hydrogen missing using PRODRG

Thu, 14 Oct 2010 05:02:32 -0700 


Jennifer Williams wrote:


Hi,


So, I did as suggested. Ran PRODRG the first time using the JME Editor 
and took the pdb file from this. Then I added the ADDHYD OAE underneath 
(actually it doesn't matter which O (OAD or OAE) is protonated as long 
as it is only one of them).


The first bit of output looked encouraging...

PRODRG> PDB mode detected.
PRODRG> Molecule complexity index: 2.00.
PRODRG> Added hydrogen on atom OAE .
PRODRG>  18 hydrogen(s) added.
PRODRG> Using charge groups.
PRODRG> Net charge on molecule:   0.000
PRODRG>  20 partial charges      0 ambiguous
PRODRG> Cannot assign type to atom ' OAE'.
ERRDRG> Error in GROMOS atom names/types.
PRODRG> Program terminated unsuccessfully, sorry!


So it understood that I wanted a hydrogen and the net charge is at last 
0(usually -1 without that hydrogen) but then it crashes! I don't 
understand why it can't assign a type to OAE. IS it because a hydrogen 
is now attached so the hybridisation has changed from sp2 to sp3?



Do I need to change the identity of OAE before putting a hydrogen on? If 
so to what?





It looks like PRODRG simply isn't working as advertised.  I can force 
protonation of N atoms without problem, but it won't work for O for some reason. 
   You have several options:


1. Write an .rtp entry for your molecule instead.

2. Add the H in manually and add the bonded parameters for it.  Since PRODRG 
charges have to be manually changed anyway, this isn't too much more work.


-Justin


Thanks

Jenny


REMARK
REMARK
REMARK  This file was generated by PRODRG version 071121.0636
REMARK  PRODRG written/copyrighted by Daan van Aalten
REMARK  and Alexander Schuettelkopf
REMARK
REMARK  Questions/comments to d...@davapc1.bioch.dundee.ac.uk
REMARK
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK
REMARK

HETATM    1  CAA DRG     1       2.360   1.610   1.840  1.00 20.00     
        C
HETATM    2  CAN DRG     1       3.580   2.340   1.260  1.00 20.00     
        C
HETATM    3  CAB DRG     1       3.330   2.650  -0.210  1.00 20.00     
        C
HETATM    4  CAJ DRG     1       4.820   1.450   1.460  1.00 20.00     
        C
HETATM    5  CAL DRG     1       6.160   2.130   1.140  1.00 20.00     
        C
HETATM    6  CAG DRG     1       6.870   1.740  -0.010  1.00 20.00     
        C
HETATM    7  CAI DRG     1       8.100   2.360  -0.300  1.00 20.00     
        C
HETATM    8  CAF DRG     1       6.640   3.140   2.010  1.00 20.00     
        C
HETATM    9  CAH DRG     1       7.870   3.760   1.720  1.00 20.00     
        C
HETATM   10  CAM DRG     1       8.600   3.370   0.570  1.00 20.00     
        C
HETATM   11  CAO DRG     1       9.930   4.110   0.310  1.00 20.00     
        C
HETATM   12  CAC DRG     1      10.120   4.580  -1.140  1.00 20.00     
        C
HETATM   13  CAK DRG     1      11.150   3.250   0.700  1.00 20.00     
        C
HETATM   14  OAE DRG     1      12.100   3.870   1.240  1.00 20.00     
        O
HETATM   15  OAD DRG     1      11.130   2.020   0.480  1.00 20.00     
        O

CONECT    1    2
CONECT    2    1    3    4
CONECT    3    2
CONECT    4    2    5
CONECT    5    4    6    8
CONECT    6    5    7
CONECT    7    6   10
CONECT    8    5    9
CONECT    9    8   10
CONECT   10    7    9   11
CONECT   11   10   12   13
CONECT   12   11
CONECT   13   11   14   15
CONECT   14   13
CONECT   15   13
END
ADDHYD OAE








Quoting "Justin A. Lemkul" <jalem...@vt.edu>:



You need to run PRODRG twice.  The first time, do not use ADDHYD.  Make
note of the atom names that PRODRG assigns.  Then run PRODRG a second
time, using ADDHYD with the atom name that PRODRG uses for the O atom
you want protonated.

-Justin

Jennifer Williams wrote:



Hi Justin,


Thanks for your answer. The ADDHYD in the FAQ sounds like exactly  
what I need however I can't get this command to work. I draw in my  
molecule using the JME editor and get this .pdb file in the PRODRG  
window.


CC(C)Cc1ccc(C(C)C(=O)O)cc1
JME 2002.05 Thu Oct 14 10:48:38 BST 2010

15 15                            V2000
   0.0000    0.0000    0.0000 C
   1.2124    2.1000    0.0000 C
   7.2746    4.2000    0.0000 C
   8.4870    0.7000    0.0000 O
   9.6995    2.8000    0.0000 O
   3.6373    2.1000    0.0000 C
   4.8497    0.0000    0.0000 C
   4.8497    2.8000    0.0000 C
   6.0622    0.7000    0.0000 C
   2.4249    0.0000    0.0000 C
   8.4870    2.1000    0.0000 C
   3.6373    0.7000    0.0000 C
   6.0622    2.1000    0.0000 C
   1.2124    0.7000    0.0000 C
   7.2746    2.8000    0.0000 C
 1 14  1  0
 2 14  1  0
 3 15  1  0
 4 11  2  0
 5 11  1  0
 6  8  1  0
 6 12  2  0
 7  9  2  0
 7 12  1  0
 8 13  2  0
 9 13  1  0
10 12  1  0
10 14  1  0
11 15  1  0
13 15  1  0
M  END


If I then try adding ADDHYD O to the window and clicking "run  
PRODRG" I get the following:


ERRDRG> Atom 'O' referenced in instruction was not found.
PRODRG> Program terminated unsuccessfully, sorry!


I've then tried renaming O to OM as there are 2 Os in my structure  
and I only want one protonated. However, no other name is  recognized 
so I get this message:


ERRDRG> Currently only N, C, O, S, P, Cl, Br, F, I are supported.
PRODRG> Program terminated unsuccessfully, sorry!


Next I tried using the PDB generated by PRODRG and repasting it  with 
the ADDHYD command into the PRODRG window.


Now the pdb looks like this:

REMARK
REMARK
REMARK  This file was generated by PRODRG version 071121.0636
REMARK  PRODRG written/copyrighted by Daan van Aalten
REMARK  and Alexander Schuettelkopf
REMARK
REMARK  Questions/comments to d...@davapc1.bioch.dundee.ac.uk
REMARK
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK
REMARK

HETATM    1  CAA DRG     1       2.360   1.610   1.840  1.00 20.00  
           C
HETATM    2  CAN DRG     1       3.580   2.340   1.260  1.00 20.00  
           C
HETATM    3  CAB DRG     1       3.330   2.650  -0.210  1.00 20.00  
           C
HETATM    4  CAJ DRG     1       4.820   1.450   1.460  1.00 20.00  
           C
HETATM    5  CAL DRG     1       6.160   2.130   1.140  1.00 20.00  
           C
HETATM    6  CAG DRG     1       6.870   1.740  -0.010  1.00 20.00  
           C
HETATM    7  CAI DRG     1       8.100   2.360  -0.300  1.00 20.00  
           C
HETATM    8  CAF DRG     1       6.640   3.140   2.010  1.00 20.00  
           C
HETATM    9  CAH DRG     1       7.870   3.760   1.720  1.00 20.00  
           C
HETATM   10  CAM DRG     1       8.600   3.370   0.570  1.00 20.00  
           C
HETATM   11  CAO DRG     1       9.930   4.110   0.310  1.00 20.00  
           C
HETATM   12  CAC DRG     1      10.120   4.580  -1.140  1.00 20.00  
           C
HETATM   13  CAK DRG     1      11.150   3.250   0.700  1.00 20.00  
           C
HETATM   14  OAE DRG     1      12.100   3.870   1.240  1.00 20.00  
           O
HETATM   15  OAD DRG     1      11.130   2.020   0.480  1.00 20.00  
           O

CONECT    1    2
CONECT    2    1    3    4
CONECT    3    2
CONECT    4    2    5
CONECT    5    4    6    8
CONECT    6    5    7
CONECT    7    6   10
CONECT    8    5    9
CONECT    9    8   10
CONECT   10    7    9   11
CONECT   11   10   12   13
CONECT   12   11
CONECT   13   11   14   15
CONECT   14   13
CONECT   15   13
END


I've tried changing the HETATM to OM and using ADDHYD OM and then  
played around with various other things like renaming the atom  
symbol at the end of the line and even the OAD, DRG but I always  get 
the following:


ERRDRG> Atom 'OM' referenced in instruction was not found.
PRODRG> Program terminated unsuccessfully, sorry!

I am using the PRODRG beta server available online at

http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta


Will I fare any better if I use the source code or is there  
something obvious I am doing wrong? Does the ADDHYD have to be  added 
in any particular location of the pdb file? I have tried a  few 
random positions including at the very top, very bottom and  just 
beneath the O to be protonated. Nothing worked.


Any ideas much appreciated,

Jenny



Quoting "Justin A. Lemkul" <jalem...@vt.edu>:




Jennifer Williams wrote:



Hi,


I am trying to get a .itp file for a simple molecule (Ibuprofen).   
This contains a COOH group.



THe problem is that PRODRG removes the polar hydrogen of the COOH   
from the .pdb file and generates a .itp file without it.



I am not concerned about the other aromatic hydrogens but I  
really  need the polar hydrogen modelled explicitly.


Is there a fix for this within PRODRG?


I know I can use pdb2gmx to add hydrogens but the residue names  
of  the pdb file are not recognized by the existing forcefields  so 
I  usually bypass using pdb2gmx.





Have a look at the PRODRG FAQ - there's an entry there for modifying
protonation state.

-Justin


Thanks

Jenny



Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
Sanderson Building
The King's Buildings
Mayfield Road
Edinburgh, EH9 3JL, United Kingdom
Phone: ++44 (0)131 650 4 861




--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
Sanderson Building
The King's Buildings
Mayfield Road
Edinburgh, EH9 3JL, United Kingdom
Phone: ++44 (0)131 650 4 861




--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
--
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Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists




Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
Sanderson Building
The King's Buildings
Mayfield Road
Edinburgh, EH9 3JL, United Kingdom
Phone: ++44 (0)131 650 4 861




--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
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