[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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