[gmx-users] distorted phosphate group
Daniel Rigden
drigden at liverpool.ac.uk
Thu Jul 7 11:15:57 CEST 2005
Dear all
We're trying to do a simulation of a protein with bound
2-phosphoglycerate. I've used PRODRG to get the itp file. It does a
great job, except for an unexpected problem with the phospho group - it
becomes distorted after minimisation. I can't see why this should be,
but perhaps someone else can. The distortion was a little less when I
increased the Improper for the tetrahedral P O3P O4P O2P ten-fold,
but the problem is still there.
Here is the distorted ligand, after minimization and limited MD when the
problem becomes even more obvious.
ATOM 5061 O3P 2PG 512 45.450 40.700 34.640 1.00 0.00
ATOM 5062 P 2PG 512 44.450 40.750 35.900 1.00 0.00
ATOM 5063 O4P 2PG 512 45.980 40.380 36.230 1.00 0.00
ATOM 5064 O2P 2PG 512 44.480 39.460 36.630 1.00 0.00
ATOM 5065 O1P 2PG 512 44.770 41.960 36.910 1.00 0.00
ATOM 5066 C2 2PG 512 43.670 42.820 37.200 1.00 0.00
ATOM 5067 C1 2PG 512 42.660 42.220 38.180 1.00 0.00
ATOM 5068 O2 2PG 512 41.540 41.860 37.760 1.00 0.00
ATOM 5069 O1 2PG 512 43.010 42.100 39.370 1.00 0.00
ATOM 5070 C3 2PG 512 44.250 44.110 37.790 1.00 0.00
ATOM 5071 O3 2PG 512 43.260 45.010 38.290 1.00 0.00
ATOM 5072 HAA 2PG 512 43.040 45.680 37.580 1.00 0.00
Here is the original PRODRG output. Thanks in advance for your help.
Daniel.
;
;
; This file was generated by PRODRG version 050304.0528
; PRODRG written/copyrighted by Daan van Aalten
;
; 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
2PG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OA 1 2PG O3P 1 -1.094 15.9994
2 P 1 2PG P 1 1.172 30.9738
3 OA 1 2PG O4P 1 -1.094 15.9994
4 OM 1 2PG O2P 1 -0.791 15.9994
5 OS 1 2PG O1P 1 -0.193 15.9994
6 CH1 1 2PG C2 2 0.123 13.0190
7 C 1 2PG C1 2 0.365 12.0110
8 OM 1 2PG O2 2 -0.744 15.9994
9 OM 1 2PG O1 2 -0.744 15.9994
10 CH2 1 2PG C3 3 0.080 14.0270
11 OA 1 2PG O3 3 -0.139 15.9994
12 HO 1 2PG HAA 3 0.059 1.0080
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.161 251040.0 0.161 251040.0 ; O3P P
2 3 1 0.161 251040.0 0.161 251040.0 ; P O4P
2 4 1 0.148 376560.0 0.148 376560.0 ; P O2P
2 5 1 0.161 251040.0 0.161 251040.0 ; P O1P
5 6 1 0.143 334720.0 0.143 334720.0 ; O1P C2
6 7 1 0.153 334720.0 0.153 334720.0 ; C2 C1
6 10 1 0.153 334720.0 0.153 334720.0 ; C2 C3
7 8 1 0.125 418400.0 0.125 418400.0 ; C1 O2
7 9 1 0.125 418400.0 0.125 418400.0 ; C1 O1
10 11 1 0.143 334720.0 0.143 334720.0 ; C3 O3
11 12 1 0.100 313800.0 0.100 313800.0 ; O3 HAA
[ pairs ]
; ai aj fu c0, c1, ...
1 6 1 ; O3P C2
2 7 1 ; P C1
2 10 1 ; P C3
3 6 1 ; O4P C2
4 6 1 ; O2P C2
5 8 1 ; O1P O2
5 9 1 ; O1P O1
5 11 1 ; O1P O3
6 12 1 ; C2 HAA
7 11 1 ; C1 O3
8 10 1 ; O2 C3
9 10 1 ; O1 C3
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 1 103.0 397.5 103.0 397.5 ; O3P P
O4P
1 2 4 1 109.6 397.5 109.6 397.5 ; O3P P
O2P
1 2 5 1 103.0 397.5 103.0 397.5 ; O3P P
O1P
3 2 4 1 109.6 397.5 109.6 397.5 ; O4P P
O2P
3 2 5 1 103.0 397.5 103.0 397.5 ; O4P P
O1P
4 2 5 1 109.6 397.5 109.6 397.5 ; O2P P
O1P
2 5 6 1 120.0 397.5 120.0 397.5 ; P O1P
C2
5 6 7 1 109.5 460.2 109.5 460.2 ; O1P C2
C1
5 6 10 1 109.5 460.2 109.5 460.2 ; O1P C2
C3
7 6 10 1 109.5 460.2 109.5 460.2 ; C1 C2
C3
6 7 8 1 117.0 502.1 117.0 502.1 ; C2 C1
O2
6 7 9 1 117.0 502.1 117.0 502.1 ; C2 C1
O1
8 7 9 1 126.0 502.1 126.0 502.1 ; O2 C1
O1
6 10 11 1 109.5 460.2 109.5 460.2 ; C2 C3
O3
10 11 12 1 109.5 397.5 109.5 397.5 ; C3 O3
HAA
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
7 6 9 8 2 0.0 1673.6 0 0.0 1673.6 0 ; imp C1
C2 O1
O2
2 1 3 4 2 35.3 836.8 0 35.3 836.8 0 ; imp P
O3P O4P
O2P
6 5 10 7 2 35.3 836.8 0 35.3 836.8 0 ; imp C2
O1P C3
C1
6 5 2 1 1 0.0 1.0 3 0.0 1.0 3 ; dih C2
O1P P
O3P
6 5 2 1 1 0.0 3.1 2 0.0 3.1 2 ; dih C2
O1P P
O3P
2 5 6 10 1 0.0 1.3 3 0.0 1.3 3 ; dih P
O1P C2
C3
5 6 7 9 1 0.0 0.4 6 0.0 0.4 6 ; dih O1P
C2 C1
O1
11 10 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih O3
C3 C2
O1P
6 10 11 12 1 0.0 1.3 3 0.0 1.3 3 ; dih C2
C3 O3
HAA
--
Dr Daniel John Rigden Tel:(+44) 151 795 4467
School of Biological Sciences FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool
Crown St.,
Liverpool L69 7ZB, U.K.
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