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 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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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
--
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