[gmx-users] Self made GDP topology file.......deforms severely with LINC warning during EM and stopped

Daan van Aalten vdava at davapc1.bioch.dundee.ac.uk
Thu Nov 4 19:34:57 CET 2004


Hi Zhenting

You cannot use PRODRG topologies for anything else than the ffgmx
forcefield. If you start editing them it is not too difficult to make some
mistakes and obtain the deformed structure.

We plan to, before Xmas, release a freely downloadable version of PRODRG
which can also write out gromos96 topologies.

cheers

Daan

On Fri, 5 Nov 2004, Zhenting Gao wrote:

> Hi  gmx-users,
>
>      A GDP is in my protein complex. So I made my own Gromos 96 FF topology file for GDP.
>      First, I get the topology from PRODRG server.
>      Then I use Gaussian to recalculate the atom charge.
>      At last I refer to the topology of ATP and GUA in ffG43a1.rtp to modify the topology file for GDP.
>      However, the GDP deforms severely during the EM, and even crashes if I run a heating process.(it deforms whether I add positive ion or not. )
>      In contrast, the topology files generated by pdb2gmx for ATP and DGUA  make the structure ramain good during a 300K heating process.
>      Why it deforms? It is the wrong force parameter? Or the wrong atom charge?
>
>      Please help me to check. The topology files are listed as below.
>
> Thanks.
>
> GDP.gro
> -------------------------------------------------------------------------------
>  PRODRG COORDS
>    33
>     1GDP  O2B      1  13.796  -0.791   5.821
>     1GDP  PB       2  13.911  -0.692   5.803
>     1GDP  O3B      3  14.047  -0.756   5.808
>     1GDP  O1B      4  13.899  -0.581   5.703
>     1GDP  O3A      5  13.903  -0.603   5.936
>     1GDP  PA       6  13.884  -0.674   6.079
>     1GDP  O1A      7  13.832  -0.817   6.074
>     1GDP  O2A      8  14.009  -0.643   6.156
>     1GDP  O5'      9  13.765  -0.580   6.127
>     1GDP  C5'     10  13.801  -0.458   6.192
>     1GDP  C4'     11  13.672  -0.403   6.247
>     1GDP  O4'     12  13.568  -0.441   6.158
>     1GDP  C3'     13  13.636  -0.465   6.382
>     1GDP  O3'     14  13.660  -0.381   6.493
>     1GDP  HAA     15  13.759  -0.370   6.506
>     1GDP  C2'     16  13.487  -0.474   6.373
>     1GDP  O2'     17  13.439  -0.353   6.433
>     1GDP  HAB     18  13.339  -0.352   6.431
>     1GDP  C1'     19  13.448  -0.469   6.227
>     1GDP  N9      20  13.387  -0.597   6.187
>     1GDP  C8      21  13.442  -0.705   6.127
>     1GDP  N7      22  13.347  -0.801   6.108
>     1GDP  C5      23  13.232  -0.754   6.159
>     1GDP  C4      24  13.259  -0.620   6.214
>     1GDP  N3      25  13.162  -0.549   6.273
>     1GDP  C2      26  13.036  -0.595   6.285
>     1GDP  N2      27  12.943  -0.515   6.342
>     1GDP  HAE     28  12.968  -0.423   6.373
>     1GDP  HAD     29  12.848  -0.547   6.352
>     1GDP  N1      30  13.002  -0.717   6.239
>     1GDP  HAC     31  12.907  -0.748   6.248
>     1GDP  C6      32  13.093  -0.798   6.183
>     1GDP  O6      33  13.058  -0.909   6.144
> -------------------------------------------------------------------------------
> GDP.top
> -------------------------------------------------------------------------------
> ;      This file is modified to Gromos 96 FF on 20041104
> ;
> ;       This file was generated by PRODRG version 041015.0515
> ;       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.
> ; Include forcefield parameters
> #include "ffG43a1.itp"
> [ moleculetype ]
> ; Name nrexcl
> GDP      3
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>      1        OM     1  GDP     O2B     1   -0.941   15.9994
>      2         P     1  GDP      PB     1   1.334    30.9738
>      3        OM     1  GDP     O3B     1   -0.975   15.9994
>      4        OM     1  GDP     O1B     1   -1.043   15.9994
>      5        OA     1  GDP     O3A     2   -0.482   15.9994
>      6         P     1  GDP      PA     2   1.429    30.9738
>      7        OM     1  GDP     O1A     2   -0.852   15.9994
>      8        OM     1  GDP     O2A     2   -0.949   15.9994
>      9        OA     1  GDP     O5'     2   -0.672   15.9994
>     10       CH2     1  GDP     C5'     3   0.179    14.0270
>     11       CH1     1  GDP     C4'     3   0.362    13.0190
>     12        OA     1  GDP     O4'     3   -0.412   15.9994
>     13       CH1     1  GDP     C3'     4   0.233    13.0190
>     14        OA     1  GDP     O3'     4   -0.710   15.9994
>     15         H     1  GDP     HAA     4   0.399     1.0080
>     16       CH1     1  GDP     C2'     5   0.419    13.0190
>     17        OA     1  GDP     O2'     5   -0.686   15.9994
>     18         H     1  GDP     HAB     5   0.357     1.0080
>     19       CH1     1  GDP     C1'     5   0.140    13.0190
>     20        NR     1  GDP      N9     6   0.113    14.0067
>     21       CR1     1  GDP      C8     6   0.354    13.0190
>     22        NR     1  GDP      N7     7   -0.497   14.0067
>     23         C     1  GDP      C5     7   -0.025   12.0110
>     24         C     1  GDP      C4     7   0.245    12.0110
>     25        NR     1  GDP      N3     7   -0.822   14.0067
>     26         C     1  GDP      C2     7   1.075    12.0110
>     27        NT     1  GDP      N2     8   -1.184   14.0067
>     28         H     1  GDP     HAE     8   0.475     1.0080
>     29         H     1  GDP     HAD     8   0.454     1.0080
>     30        NR     1  GDP      N1     9   -0.791   14.0067
>     31         H     1  GDP     HAC     9   0.403     1.0080
>     32         C     1  GDP      C6     9   0.749    12.0110
>     33         O     1  GDP      O6     9   -0.679   15.9994
> [ bonds ]
> ; ai  aj  fu    c0, c1, ...
>    1   2   2 gb_23   ;0.161    251040.0    0.161    251040.0 ;   O2B   PB
>    2   3   2 gb_23   ;0.161    251040.0    0.161    251040.0 ;    PB  O3B
>    2   4   2 gb_23   ;0.148    376560.0    0.148    376560.0 ;    PB  O1B
>    2   5   2 gb_27   ;0.161    251040.0    0.161    251040.0 ;    PB  O3A
>    5   6   2 gb_27   ;0.161    251040.0    0.161    251040.0 ;   O3A   PA
>    6   7   2 gb_23   ;0.148    376560.0    0.148    376560.0 ;    PA  O1A
>    6   8   2 gb_23   ;0.148    376560.0    0.148    376560.0 ;    PA  O2A
>    6   9   2 gb_27   ;0.161    251040.0    0.161    251040.0 ;    PA  O5'
>    9  10   2 gb_19   ;0.143    251040.0    0.143    251040.0 ;   O5'  C5'
>   10  11   2 gb_25   ;0.153    251040.0    0.153    251040.0 ;   C5'  C4'
>   11  12   2 gb_19   ;0.144    251040.0    0.144    251040.0 ;   C4'  O4'
>   11  13   2 gb_25   ;0.153    334720.0    0.153    334720.0 ;   C4'  C3'
>   12  19   2 gb_19   ;0.144    251040.0    0.144    251040.0 ;   O4'  C1'
>   13  14   2 gb_19   ;0.143    334720.0    0.143    334720.0 ;   C3'  O3'
>   13  16   2 gb_25   ;0.153    334720.0    0.153    334720.0 ;   C3'  C2'
>   14  15   2 gb_1    ;0.100    313800.0    0.100    313800.0 ;   O3'  HAA
>   16  17   2 gb_19   ;0.143    334720.0    0.143    334720.0 ;   C2'  O2'
>   16  19   2 gb_25   ;0.153    334720.0    0.153    334720.0 ;   C2'  C1'
>   17  18   2 gb_1    ;0.100    313800.0    0.100    313800.0 ;   O2'  HAB
>   19  20   2 gb_21   ;0.148    251040.0    0.148    251040.0 ;   C1'   N9
>   20  21   2 gb_9    ;0.133    418400.0    0.133    418400.0 ;    N9   C8
>   20  24   2 gb_9    ;0.133    418400.0    0.133    418400.0 ;    N9   C4
>   21  22   2 gb_9    ;0.133    418400.0    0.133    418400.0 ;    C8   N7
>   22  23   2 gb_9    ;0.133    418400.0    0.133    418400.0 ;    N7   C5
>   23  24   2 gb_15   ;0.139    418400.0    0.139    418400.0 ;    C5   C4
>   23  32   2 gb_15   ;0.139    418400.0    0.139    418400.0 ;    C5   C6
>   24  25   2 gb_11   ;0.134    418400.0    0.134    418400.0 ;    C4   N3
>   25  26   2 gb_11   ;0.134    418400.0    0.134    418400.0 ;    N3   C2
>   26  27   2 gb_8    ;0.133    376560.0    0.133    376560.0 ;    C2   N2
>   26  30   2 gb_16   ;0.140    334720.0    0.140    334720.0 ;    C2   N1
>   27  28   2 gb_2    ;0.100    374468.0    0.100    374468.0 ;    N2  HAE
>   27  29   2 gb_2    ;0.100    374468.0    0.100    374468.0 ;    N2  HAD
>   30  31   2 gb_2    ;0.100    374468.0    0.100    374468.0 ;    N1  HAC
>   30  32   2 gb_16   ;0.140    334720.0    0.140    334720.0 ;    N1   C6
>   32  33   2 gb_4    ;0.123    502080.0    0.123    502080.0 ;    C6   O6
> [ pairs ]
> ; ai  aj  fu    c0, c1, ...
>    1   6   1                                           ;   O2B   PA
>    2   7   1                                           ;    PB  O1A
>    2   8   1                                           ;    PB  O2A
>    2   9   1                                           ;    PB  O5'
>    3   6   1                                           ;   O3B   PA
>    4   6   1                                           ;   O1B   PA
>    5  10   1                                           ;   O3A  C5'
>    6  11   1                                           ;    PA  C4'
>    7  10   1                                           ;   O1A  C5'
>    8  10   1                                           ;   O2A  C5'
>    9  12   1                                           ;   O5'  O4'
>    9  13   1                                           ;   O5'  C3'
>   10  14   1                                           ;   C5'  O3'
>   10  16   1                                           ;   C5'  C2'
>   10  19   1                                           ;   C5'  C1'
>   11  15   1                                           ;   C4'  HAA
>   11  17   1                                           ;   C4'  O2'
>   11  20   1                                           ;   C4'   N9
>   12  14   1                                           ;   O4'  O3'
>   12  17   1                                           ;   O4'  O2'
>   12  21   1                                           ;   O4'   C8
>   12  24   1                                           ;   O4'   C4
>   13  18   1                                           ;   C3'  HAB
>   13  20   1                                           ;   C3'   N9
>   14  17   1                                           ;   O3'  O2'
>   14  19   1                                           ;   O3'  C1'
>   15  16   1                                           ;   HAA  C2'
>   16  21   1                                           ;   C2'   C8
>   16  24   1                                           ;   C2'   C4
>   17  20   1                                           ;   O2'   N9
>   18  19   1                                           ;   HAB  C1'
>   19  22   1                                           ;   C1'   N7
>   19  23   1                                           ;   C1'   C5
>   19  25   1                                           ;   C1'   N3
>   20  26   1                                           ;    N9   C2
>   20  32   1                                           ;    N9   C6
>   21  25   1                                           ;    C8   N3
>   21  32   1                                           ;    C8   C6
>   22  25   1                                           ;    N7   N3
>   22  30   1                                           ;    N7   N1
>   22  33   1                                           ;    N7   O6
>   23  26   1                                           ;    C5   C2
>   23  31   1                                           ;    C5  HAC
>   24  27   1                                           ;    C4   N2
>   24  30   1                                           ;    C4   N1
>   24  33   1                                           ;    C4   O6
>   25  28   1                                           ;    N3  HAE
>   25  29   1                                           ;    N3  HAD
>   25  31   1                                           ;    N3  HAC
>   25  32   1                                           ;    N3   C6
>   26  33   1                                           ;    C2   O6
>   27  31   1                                           ;    N2  HAC
>   27  32   1                                           ;    N2   C6
>   28  30   1                                           ;   HAE   N1
>   29  30   1                                           ;   HAD   N1
>   31  33   1                                           ;   HAC   O6
> [ angles ]
> ; ai  aj  ak  fu    c0, c1, ...
>    1   2   3   2 ga_13    ;103.0       397.5    103.0       397.5 ;   O2B   PB  O3B
>    1   2   4   2 ga_13    ;109.6       397.5    109.6       397.5 ;   O2B   PB  O1B
>    1   2   5   2 ga_13    ;103.0       397.5    103.0       397.5 ;   O2B   PB  O3A
>    3   2   4   2 ga_13    ;109.6       397.5    109.6       397.5 ;   O3B   PB  O1B
>    3   2   5   2 ga_13    ;103.0       397.5    103.0       397.5 ;   O3B   PB  O3A
>    4   2   5   2 ga_13    ;109.6       397.5    109.6       397.5 ;   O1B   PB  O3A
>    2   5   6   2 ga_25    ;120.0       397.5    120.0       397.5 ;    PB  O3A   PA
>    5   6   7   2 ga_13    ;109.6       397.5    109.6       397.5 ;   O3A   PA  O1A
>    5   6   8   2 ga_13    ;109.6       397.5    109.6       397.5 ;   O3A   PA  O2A
>    5   6   9   2 ga_4     ;103.0       397.5    103.0       397.5 ;   O3A   PA  O5'
>    7   6   8   2 ga_28    ;120.0       585.8    120.0       585.8 ;   O1A   PA  O2A
>    7   6   9   2 ga_13    ;109.6       397.5    109.6       397.5 ;   O1A   PA  O5'
>    8   6   9   2 ga_13    ;109.6       397.5    109.6       397.5 ;   O2A   PA  O5'
>    6   9  10   2 ga_25    ;120.0       397.5    120.0       397.5 ;    PA  O5'  C5'
>    9  10  11   2 ga_8     ;111.0       460.2    111.0       460.2 ;   O5'  C5'  C4'
>   10  11  12   2 ga_8     ;109.5       284.5    109.5       284.5 ;   C5'  C4'  O4'
>   10  11  13   2 ga_7     ;109.5       251.0    109.5       251.0 ;   C5'  C4'  C3'
>   12  11  13   2 ga_8     ;104.0       460.2    104.0       460.2 ;   O4'  C4'  C3'
>   11  12  19   2 ga_9     ;104.0       460.2    104.0       460.2 ;   C4'  O4'  C1'
>   11  13  14   2 ga_8     ;109.5       460.2    109.5       460.2 ;   C4'  C3'  O3'
>   11  13  16   2 ga_7     ;104.0       460.2    104.0       460.2 ;   C4'  C3'  C2'
>   14  13  16   2 ga_8     ;109.5       460.2    109.5       460.2 ;   O3'  C3'  C2'
>   13  14  15   2 ga_11    ;109.5       397.5    109.5       397.5 ;   C3'  O3'  HAA
>   13  16  17   2 ga_8     ;109.5       460.2    109.5       460.2 ;   C3'  C2'  O2'
>   13  16  19   2 ga_7     ;104.0       460.2    104.0       460.2 ;   C3'  C2'  C1'
>   17  16  19   2 ga_8     ;109.5       460.2    109.5       460.2 ;   O2'  C2'  C1'
>   16  17  18   2 ga_11    ;109.5       397.5    109.5       397.5 ;   C2'  O2'  HAB
>   12  19  16   2 ga_8     ;104.0       460.2    104.0       460.2 ;   O4'  C1'  C2'
>   12  19  20   2 ga_8     ;109.5       284.5    109.5       284.5 ;   O4'  C1'   N9
>   16  19  20   2 ga_8     ;109.5       284.5    109.5       284.5 ;   C2'  C1'   N9
>   19  20  21   2 ga_36    ;126.0       418.4    126.0       418.4 ;   C1'   N9   C8
>   19  20  24   2 ga_36    ;126.0       418.4    126.0       418.4 ;   C1'   N9   C4
>   21  20  24   2 ga_6     ;108.0       418.4    108.0       418.4 ;    C8   N9   C4
>   20  21  22   2 ga_6     ;108.0       418.4    108.0       418.4 ;    N9   C8   N7
>   21  22  23   2 ga_6     ;108.0       418.4    108.0       418.4 ;    C8   N7   C5
>   22  23  24   2 ga_6     ;108.0       418.4    108.0       418.4 ;    N7   C5   C4
>   22  23  32   2 ga_38    ;132.0       418.4    132.0       418.4 ;    N7   C5   C6
>   24  23  32   2 ga_26    ;120.0       418.4    120.0       418.4 ;    C4   C5   C6
>   20  24  23   2 ga_6     ;108.0       418.4    108.0       418.4 ;    N9   C4   C5
>   20  24  25   2 ga_38    ;132.0       418.4    132.0       418.4 ;    N9   C4   N3
>   23  24  25   2 ga_26    ;120.0       418.4    120.0       418.4 ;    C5   C4   N3
>   24  25  26   2 ga_26    ;120.0       418.4    120.0       418.4 ;    C4   N3   C2
>   25  26  27   2 ga_26    ;120.0       418.4    120.0       418.4 ;    N3   C2   N2
>   25  26  30   2 ga_26    ;120.0       418.4    120.0       418.4 ;    N3   C2   N1
>   27  26  30   2 ga_26    ;120.0       418.4    120.0       418.4 ;    N2   C2   N1
>   26  27  28   2 ga_22    ;120.0       292.9    120.0       292.9 ;    C2   N2  HAE
>   26  27  29   2 ga_22    ;120.0       292.9    120.0       292.9 ;    C2   N2  HAD
>   28  27  29   2 ga_23    ;120.0       334.7    120.0       334.7 ;   HAE   N2  HAD
>   26  30  31   2 ga_24    ;120.0       376.6    120.0       376.6 ;    C2   N1  HAC
>   26  30  32   2 ga_26    ;120.0       418.4    120.0       418.4 ;    C2   N1   C6
>   31  30  32   2 ga_24    ;120.0       376.6    120.0       376.6 ;   HAC   N1   C6
>   23  32  30   2 ga_26    ;120.0       418.4    120.0       418.4 ;    C5   C6   N1
>   23  32  33   2 ga_26    ;120.0       418.4    120.0       418.4 ;    C5   C6   O6
>   30  32  33   2 ga_26    ;120.0       418.4    120.0       418.4 ;    N1   C6   O6
> [ dihedrals ]
> ; ai  aj  ak  al  fu    c0, c1, m, ...
>   19  21  24  20  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    N9  C1'   C8   C4
>   32  24  22  23  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    C5   C6   C4   N7
>   25  23  20  24  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    C4   N3   C5   N9
>   25  30  27  26  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    C2   N3   N1   N2
>   26  28  29  27  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    N2   C2  HAE  HAD
>   32  31  26  30  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    N1   C6  HAC   C2
>   23  30  33  32  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    C6   C5   N1   O6
>    1   4   3   2  2  gi_2     ; 35.3  836.8 0     35.3  836.8 0 ; imp    PB  O2B  O1B  O3B
>    5   8   7   6  2  gi_2     ; 35.3  836.8 0     35.3  836.8 0 ; imp    PA  O3A  O2A  O1A
>   10  13  12  11  2  gi_2     ; 35.3  836.8 0     35.3  836.8 0 ; imp   C4'  C5'  C3'  O4'
>   11  16  14  13  2  gi_2     ; 35.3  836.8 0     35.3  836.8 0 ; imp   C3'  C4'  C2'  O3'
>   13  19  17  16  2  gi_2     ; 35.3  836.8 0     35.3  836.8 0 ; imp   C2'  C3'  C1'  O2'
>   12  16  20  19  2  gi_2     ; 35.3  836.8 0     35.3  836.8 0 ; imp   C1'  O4'  C2'   N9
>   21  22  23  20  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    N9   C8   N7   C5
>   22  23  24  21  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    C8   N7   C5   C4
>   23  24  20  22  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    N7   C5   C4   N9
>   24  20  21  23  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    C5   C4   N9   C8
>   20  21  22  24  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    C4   N9   C8   N7
>   24  25  26  23  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    C5   C4   N3   C2
>   25  26  30  24  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    C4   N3   C2   N1
>   26  30  32  25  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    N3   C2   N1   C6
>   30  32  23  26  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    C2   N1   C6   C5
>   32  23  24  30  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    N1   C6   C5   C4
>   23  24  25  32  2  gi_1     ;  0.0 1673.6 0      0.0 1673.6 0 ; imp    C6   C5   C4   N3
>    5   2   1   6  1  gd_11    ;  0.0    1.0 3      0.0    1.0 3 ; dih    PA  O3A   PB  O2B
>    5   2   1   6  1  gd_9     ;  0.0    3.1 2      0.0    3.1 2 ; dih    PA  O3A   PB  O2B
>    5   6   9   2  1  gd_11    ;  0.0    1.0 3      0.0    1.0 3 ; dih    PB  O3A   PA  O5'
>    5   6   9   2  1  gd_9     ;  0.0    3.1 2      0.0    3.1 2 ; dih    PB  O3A   PA  O5'
>    9   6   5  10  1  gd_9     ;  0.0    1.0 3      0.0    1.0 3 ; dih   C5'  O5'   PA  O3A
>    9   6   5  10  1  gd_11    ;  0.0    3.1 2      0.0    3.1 2 ; dih   C5'  O5'   PA  O3A
>    9  10  11   6  1  gd_14    ;  0.0    3.8 3      0.0    3.8 3 ; dih    PA  O5'  C5'  C4'
>   11  10   9  13  1  gd_7     ;  0.0    5.9 3      0.0    5.9 3 ; dih   C3'  C4'  C5'  O5'
>   11  12  19  10  1  gd_14    ;  0.0    3.8 3      0.0    3.8 3 ; dih   C5'  C4'  O4'  C1'
>   11  13  16  10  1  gd_17    ;  0.0    5.9 3      0.0    5.9 3 ; dih   C5'  C4'  C3'  C2'
>   19  12  11  20  1  gd_14    ;  0.0    3.8 3      0.0    3.8 3 ; dih    N9  C1'  O4'  C4'
>   13  14  15  11  1  gd_12    ;  0.0    1.3 3      0.0    1.3 3 ; dih   C4'  C3'  O3'  HAA
>   16  13  11  19  1  gd_17    ;  0.0    5.9 3      0.0    5.9 3 ; dih   C1'  C2'  C3'  C4'
>   16  17  18  13  1  gd_12    ;  0.0    1.3 3      0.0    1.3 3 ; dih   C3'  C2'  O2'  HAB
>   16  19  20  13  1  gd_7     ;  0.0    5.9 3      0.0    5.9 3 ; dih   C3'  C2'  C1'   N9
>   19  20  24  12  1  gd_6     ;  0.0    0.0 2      0.0    0.0 2 ; dih   O4'  C1'   N9   C4
>   26  27  29  25  1  gd_4     ;180.0   33.5 2    180.0   33.5 2 ; dih    N3   C2   N2  HAD
> ; Include Position restraint file
> #ifdef POSRES_GDP
> #include "posre_gdp.itp"
> #endif
> ; Include water topology
> #include "spc.itp"
> ; Include generic topology for ions
> #include "ions.itp"
> [ system ]
> ; Name
> GDP in water
> [ molecules ]
> ; Compound        #mols
> GDP                 1
> SOL              1838
> -------------------------------------------------------------------------------
> EM_gdp.mdp
> -------------------------------------------------------------------------------
> title               =  mitwasser
> cpp                 =  /lib/cpp
> define              =  -DFLEXIBLE -DPOSRES_GDP
> constraints         =  none
> integrator          =  l-bfgs
> dt                  =  0.002    ; ps !
> nsteps              =  5000
> nstlist             =  5 ;originally this is set to 10
> ns_type             =  grid
> coulombtype         = Switch
> vdw-type            = Switch
> rlist               =  1.2
> rcoulomb            =  1.0
> rvdw                =  1.0
> ;http://www.gromacs.org/pipermail/gmx-users/2004-May/010608.html
> ;       Energy minimizing stuff
> ;
> emtol               =  10.0
> emstep              =  0.01
> epsilon_r           = 1
> -------------------------------------------------------------------------------
> Deformed_gdp.pdb
> -------------------------------------------------------------------------------
> HEADER    GDP in water
> MODEL        1
> ATOM      1  O2B GDP     1      24.340  16.030  15.246  1.00  0.00
> ATOM      2  PB  GDP     1      25.390  17.010  15.440  1.00  0.00
> ATOM      3  O3B GDP     1      26.840  16.840  15.446  1.00  0.00
> ATOM      4  O1B GDP     1      25.250  18.190  14.580  1.00  0.00
> ATOM      5  O3A GDP     1      24.990  17.830  16.606  1.00  0.00
> ATOM      6  PA  GDP     1      25.280  16.740  17.586  1.00  0.00
> ATOM      7  O1A GDP     1      24.060  16.120  18.146  1.00  0.00
> ATOM      8  O2A GDP     1      26.540  16.800  18.360  1.00  0.00
> ATOM      9  O5' GDP     1      25.050  17.730  18.860  1.00  0.00
> ATOM     10  C5' GDP     1      24.480  19.060  18.866  1.00  0.00
> ATOM     11  C4' GDP     1      23.090  18.920  19.460  1.00  0.00
> ATOM     12  O4' GDP     1      22.040  18.880  18.480  1.00  0.00
> ATOM     13  C3' GDP     1      22.690  19.970  20.500  1.00  0.00
> ATOM     14  O3' GDP     1      23.340  19.900  21.820  1.00  0.00
> ATOM     15  HAA GDP     1      24.330  20.130  21.720  1.00  0.00
> ATOM     16  C2' GDP     1      21.150  19.890  20.280  1.00  0.00
> ATOM     17  O2' GDP     1      20.310  19.760  21.440  1.00  0.00
> ATOM     18  HAB GDP     1      19.750  20.600  21.480  1.00  0.00
> ATOM     19  C1' GDP     1      21.070  18.600  19.480  1.00  0.00
> ATOM     20  N9  GDP     1      20.040  17.610  19.046  1.00  0.00
> ATOM     21  C8  GDP     1      20.430  16.580  18.280  1.00  0.00
> ATOM     22  N7  GDP     1      19.510  15.630  18.286  1.00  0.00
> ATOM     23  C5  GDP     1      18.500  16.110  19.046  1.00  0.00
> ATOM     24  C4  GDP     1      18.770  17.430  19.526  1.00  0.00
> ATOM     25  N3  GDP     1      17.600  18.240  20.140  1.00  0.00
> ATOM     26  C2  GDP     1      16.620  17.910  19.380  1.00  0.00
> ATOM     27  N2  GDP     1      16.220  18.220  20.286  1.00  0.00
> ATOM     28  HAE GDP     1      17.430  18.290  20.226  1.00  0.00
> ATOM     29  HAD GDP     1      15.300  18.360  20.706  1.00  0.00
> ATOM     30  N1  GDP     1      16.200  16.710  19.266  1.00  0.00
> ATOM     31  HAC GDP     1      15.320  16.520  19.640  1.00  0.00
> ATOM     32  C6  GDP     1      17.140  15.770  19.166  1.00  0.00
> ATOM     33  O6  GDP     1      16.710  14.660  19.460  1.00  0.00
> TER      34      GDP     1
> ENDMDL
> END
> -------------------------------------------------------------------------------¡¡¡¡¡¡¡¡¡¡¡¡¡¡
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡
>
> Yours sincerely,
> Zhenting Gao
> zhentg at 163.com
> 2004-11-3
>
> ------------------------------------
> Drug Discovery and Design Center,
> Shanghai Institute of Materia Medica,
> Chinese Academy of Science
> P.R. China
> URL http://www.dddc.ac.cn/group/zhentg.htm
>



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