[gmx-users] Polar Hydrogen missing using PRODRG
Jennifer Williams
Jennifer.Williams at ed.ac.uk
Thu Oct 14 12:08:55 CEST 2010
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 dava at 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" <jalemkul at 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
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