[gmx-users] Polar Hydrogen missing using PRODRG
Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 14 12:52:44 CEST 2010
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 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
>
>
--
========================================
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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