[gmx-users] Polar Hydrogen missing using PRODRG
Jennifer Williams
Jennifer.Williams at ed.ac.uk
Thu Oct 14 13:54:27 CEST 2010
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?
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 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
ADDHYD OAE
Quoting "Justin A. Lemkul" <jalemkul at 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 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> 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
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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
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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