[gmx-users] Polar Hydrogen missing using PRODRG
Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 14 14:01:10 CEST 2010
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 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
>>>>
>>>> ========================================
>>>> --
>>>> 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
>>>> interface or send it to gmx-users-request at 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
>>
>> ========================================
>> --
>> 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
>> interface or send it to gmx-users-request at 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
========================================
More information about the gromacs.org_gmx-users
mailing list