[gmx-users] parameters for Glucose-6-phosphate
Francesco Carbone
fra.carbone8 at gmail.com
Fri Apr 29 18:09:40 CEST 2016
Good afternoon,
I'd like to run a dynamics with a protein (2bhl.pdb) and its substrate
(Glucose-6-phosphate ) to observe how mutants affects the binding.
Following Justin tutorial (thank you Justing for providing it), I use
PRODRG to generate the topology for G6P and I then included in the protein
topology.
; Include ligand topology
#include "bg6.itp"
BG6 1
The problem that I'm having is a mismatch between the number of atoms in
the coordinated and the topology once I try to add ions to the system.
Fatal error:
number of coordinates in coordinate file (solv.gro, 226651)
does not match topology (topol.top, 226644)
THis should be connected with a discrepancy between ligand.pdb and
ligand.itp, which have 20 and 27 atoms respectively.
I tried to remove from the ligand.pdb the 7 atoms that do not have a
counterpart in ligand.itp, but I always get a mismatch:
Fatal error:
number of coordinates in coordinate file (solv.gro, 226663)
does not match topology (topol.top, 226642)
How can I fix this?
below I pasted the pdb and itp files for the Glucose-6-phosphate
Thank you,
Francesco
------------------ begin FILES ------------------
PRODRG COORDS
27
1BG6 O1P 1 0.311 12.421 1.455
1BG6 P 2 0.384 12.355 1.345
1BG6 O2P 3 0.515 12.411 1.305
1BG6 O3P 4 0.376 12.208 1.349
1BG6 O6 5 0.295 12.402 1.219
1BG6 C6 6 0.153 12.391 1.232
1BG6 H61 7 0.123 12.288 1.211
1BG6 H62 8 0.128 12.426 1.332
1BG6 C5 9 0.082 12.483 1.136
1BG6 H5 10 0.096 12.586 1.170
1BG6 O5 11 0.146 12.465 1.008
1BG6 C1 12 0.090 12.551 0.908
1BG6 H11 13 0.105 12.655 0.938
1BG6 O1 14 0.155 12.529 0.787
1BG6 H12 15 0.141 12.434 0.759
1BG6 C2 16 -0.058 12.528 0.892
1BG6 H21 17 -0.075 12.425 0.861
1BG6 O2 18 -0.109 12.617 0.794
1BG6 H22 19 -0.094 12.712 0.823
1BG6 C3 20 -0.127 12.551 1.026
1BG6 H31 21 -0.108 12.653 1.059
1BG6 O3 22 -0.268 12.529 1.014
1BG6 H32 23 -0.285 12.435 0.983
1BG6 C4 24 -0.067 12.454 1.127
1BG6 H41 25 -0.081 12.352 1.092
1BG6 O4 26 -0.127 12.472 1.254
1BG6 H42 27 -0.113 12.567 1.284
0.95014 0.95014 0.95014
;
;
; This file was generated by PRODRG version AA100323.0717
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
;
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, 1355--1363.
;
;
[ moleculetype ]
; Name nrexcl
BG6 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 BG6 O1P 1 -0.715 15.9994
2 P 1 BG6 P 1 1.318 30.9738
3 OM 1 BG6 O2P 1 -0.714 15.9994
4 OM 1 BG6 O3P 1 -0.714 15.9994
5 OA 1 BG6 O6 1 -0.197 15.9994
6 CH2 1 BG6 C6 1 0.022 14.0270
7 CH1 1 BG6 C5 2 0.195 13.0190
8 OA 1 BG6 O5 2 -0.195 15.9994
9 CH1 1 BG6 C1 2 0.195 13.0190
10 OA 1 BG6 O1 2 -0.203 15.9994
11 H 1 BG6 H12 2 0.008 1.0080
12 CH1 1 BG6 C2 3 0.146 13.0190
13 OA 1 BG6 O2 3 -0.156 15.9994
14 H 1 BG6 H22 3 0.010 1.0080
15 CH1 1 BG6 C3 3 0.146 13.0190
16 OA 1 BG6 O3 3 -0.156 15.9994
17 H 1 BG6 H32 3 0.010 1.0080
18 CH1 1 BG6 C4 4 0.146 13.0190
19 OA 1 BG6 O4 4 -0.156 15.9994
20 H 1 BG6 H42 4 0.010 1.0080
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.148 8600000.0 0.148 8600000.0 ; P O1P
2 3 2 0.148 8600000.0 0.148 8600000.0 ; P O2P
2 4 2 0.148 8600000.0 0.148 8600000.0 ; P O3P
2 5 2 0.161 4840000.0 0.161 4840000.0 ; P O6
6 5 2 0.143 8180000.0 0.143 8180000.0 ; C6 O6
7 6 2 0.153 7150000.0 0.153 7150000.0 ; C5 C6
7 8 2 0.144 6100000.0 0.144 6100000.0 ; C5 O5
7 18 2 0.152 5430000.0 0.152 5430000.0 ; C5 C4
9 8 2 0.144 6100000.0 0.144 6100000.0 ; C1 O5
9 10 2 0.144 6100000.0 0.144 6100000.0 ; C1 O1
9 12 2 0.152 5430000.0 0.152 5430000.0 ; C1 C2
10 11 2 0.100 15700000.0 0.100 15700000.0 ; O1 H12
12 13 2 0.144 6100000.0 0.144 6100000.0 ; C2 O2
12 15 2 0.152 5430000.0 0.152 5430000.0 ; C2 C3
13 14 2 0.100 15700000.0 0.100 15700000.0 ; O2 H22
15 16 2 0.144 6100000.0 0.144 6100000.0 ; C3 O3
15 18 2 0.152 5430000.0 0.152 5430000.0 ; C3 C4
16 17 2 0.100 15700000.0 0.100 15700000.0 ; O3 H32
18 19 2 0.144 6100000.0 0.144 6100000.0 ; C4 O4
19 20 2 0.100 15700000.0 0.100 15700000.0 ; O4 H42
[ pairs ]
; ai aj fu c0, c1, ...
1 6 1 ; O1P C6
2 7 1 ; P C5
3 6 1 ; O2P C6
4 6 1 ; O3P C6
5 8 1 ; O6 O5
5 18 1 ; O6 C4
6 9 1 ; C6 C1
6 15 1 ; C6 C3
6 19 1 ; C6 O4
7 10 1 ; C5 O1
7 12 1 ; C5 C2
7 16 1 ; C5 O3
7 20 1 ; C5 H42
8 11 1 ; O5 H12
8 13 1 ; O5 O2
8 15 1 ; O5 C3
8 19 1 ; O5 O4
9 14 1 ; C1 H22
9 16 1 ; C1 O3
9 18 1 ; C1 C4
10 13 1 ; O1 O2
10 15 1 ; O1 C3
11 12 1 ; H12 C2
12 17 1 ; C2 H32
12 19 1 ; C2 O4
13 16 1 ; O2 O3
13 18 1 ; O2 C4
14 15 1 ; H22 C3
15 20 1 ; C3 H42
16 19 1 ; O3 O4
17 18 1 ; H32 C4
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 120.0 780.0 120.0 780.0 ; O1P P
O2P
1 2 4 2 120.0 780.0 120.0 780.0 ; O1P P
O3P
1 2 5 2 109.6 450.0 109.6 450.0 ; O1P P
O6
3 2 4 2 120.0 780.0 120.0 780.0 ; O2P P
O3P
3 2 5 2 109.6 450.0 109.6 450.0 ; O2P P
O6
4 2 5 2 109.6 450.0 109.6 450.0 ; O3P P
O6
2 5 6 2 120.0 530.0 120.0 530.0 ; P O6
C6
5 6 7 2 109.5 520.0 109.5 520.0 ; O6 C6
C5
6 7 8 2 109.5 320.0 109.5 320.0 ; C6 C5
O5
6 7 18 2 109.5 520.0 109.5 520.0 ; C6 C5
C4
8 7 18 2 109.5 520.0 109.5 520.0 ; O5 C5
C4
7 8 9 2 109.5 380.0 109.5 380.0 ; C5 O5
C1
8 9 10 2 109.5 320.0 109.5 320.0 ; O5 C1
O1
8 9 12 2 109.5 520.0 109.5 520.0 ; O5 C1
C2
10 9 12 2 109.5 520.0 109.5 520.0 ; O1 C1
C2
9 10 11 2 109.5 450.0 109.5 450.0 ; C1 O1
H12
9 12 13 2 109.5 520.0 109.5 520.0 ; C1 C2
O2
9 12 15 2 109.5 520.0 109.5 520.0 ; C1 C2
C3
13 12 15 2 109.5 520.0 109.5 520.0 ; O2 C2
C3
12 13 14 2 109.5 450.0 109.5 450.0 ; C2 O2
H22
12 15 16 2 109.5 520.0 109.5 520.0 ; C2 C3
O3
12 15 18 2 109.5 520.0 109.5 520.0 ; C2 C3
C4
16 15 18 2 109.5 520.0 109.5 520.0 ; O3 C3
C4
15 16 17 2 109.5 450.0 109.5 450.0 ; C3 O3
H32
7 18 15 2 109.5 520.0 109.5 520.0 ; C5 C4
C3
7 18 19 2 109.5 520.0 109.5 520.0 ; C5 C4
O4
15 18 19 2 109.5 520.0 109.5 520.0 ; C3 C4
O4
18 19 20 2 109.5 450.0 109.5 450.0 ; C4 O4
H42
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 1 4 3 2 35.3 334.8 35.3 334.8 ; imp P O1P
O3P O2P
7 6 18 8 2 35.3 334.8 35.3 334.8 ; imp C5 C6
C4 O5
9 8 12 10 2 35.3 334.8 35.3 334.8 ; imp C1 O5
C2 O1
12 9 13 15 2 35.3 334.8 35.3 334.8 ; imp C2 C1
O2 C3
15 12 18 16 2 35.3 334.8 35.3 334.8 ; imp C3 C2
C4 O3
18 19 7 15 2 35.3 334.8 35.3 334.8 ; imp C4 O4
C5 C3
6 5 2 1 1 0.0 3.1 2 0.0 3.1 2 ; dih C6 O6
P O1P
7 6 5 2 1 0.0 1.3 3 0.0 1.3 3 ; dih C5 C6
O6 P
18 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih C4 C5
C6 O6
6 7 8 9 1 0.0 3.8 3 0.0 3.8 3 ; dih C6 C5
O5 C1
19 18 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih O4 C4
C5 C6
12 9 8 7 1 0.0 3.8 3 0.0 3.8 3 ; dih C2 C1
O5 C5
8 9 10 11 1 0.0 1.3 3 0.0 1.3 3 ; dih O5 C1
O1 H12
15 12 9 8 1 0.0 5.9 3 0.0 5.9 3 ; dih C3 C2
C1 O5
9 12 13 14 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2
O2 H22
18 15 12 9 1 0.0 5.9 3 0.0 5.9 3 ; dih C4 C3
C2 C1
12 15 16 17 1 0.0 1.3 3 0.0 1.3 3 ; dih C2 C3
O3 H32
19 18 15 12 1 0.0 5.9 3 0.0 5.9 3 ; dih O4 C4
C3 C2
7 18 19 20 1 0.0 1.3 3 0.0 1.3 3 ; dih C5 C4
O4 H42
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