[gmx-users] if PRODRG calculate incorrectly

[ahmet yıldırım]

Dear users,
I have a problem related to PRODRG.

Chirality:NO
Full charges: YES
Energy minimization: NO

*İnput file name:TRS.pdb*
HETATM 1803  C   TRS B 232      38.588  -4.733  65.956  1.00 17.99
C
ANISOU 1803  C   TRS B 232     2126   1948   2760   -378     45    -81
C
HETATM 1804  C1  TRS B 232      40.103  -5.057  65.899  1.00 16.81
C
ANISOU 1804  C1  TRS B 232     1642   1577   3168   -531    171    120
C
HETATM 1805  C2  TRS B 232      37.795  -5.994  66.343  1.00 20.76
C
ANISOU 1805  C2  TRS B 232     2790   2021   3077     67    141   -408
C
HETATM 1806  C3  TRS B 232      38.160  -3.717  67.031  1.00 16.86
C
ANISOU 1806  C3  TRS B 232     2240   1557   2611   -491      8   -192
C
HETATM 1807  N   TRS B 232      38.227  -4.154  64.652  1.00 18.26
N
ANISOU 1807  N   TRS B 232     2336   2520   2083   -166     46   -112
N
HETATM 1808  O1  TRS B 232      40.741  -4.020  65.158  1.00 17.53
O
ANISOU 1808  O1  TRS B 232     1921   1579   3163   -225    147    197
O
HETATM 1809  O2  TRS B 232      37.871  -6.803  65.211  1.00 23.91
O
ANISOU 1809  O2  TRS B 232     3018   2456   3610    -48    -86   -450
O
HETATM 1810  O3  TRS B 232      38.871  -2.531  66.874  1.00 18.28
O
ANISOU 1810  O3  TRS B 232     2677   1594   2673    197     -4    -52
O

I get the output *as the following file1.itp* from your PRODRG server for
TRS ligand before 3-4 months. I think this calculate is correct:
*file1.itp*
................
[ moleculetype ]
; Name nrexcl
TRS      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1        OA     1  TRS      O1     1   -0.240  15.9994
     2        H      1  TRS     HAA     1    0.052   1.0080
     3       CH2     1  TRS      C1     1    0.061  14.0270
     4       CH1     1  TRS       C     1    0.127  12.0110
     5       CH2     1  TRS      C3     2    0.090  14.0270
     6        OA     1  TRS      O3     2   -0.165  15.9994
     7        H      1  TRS     HAC     2    0.075   1.0080
     8        NL     1  TRS       N     3    0.876  14.0067
     9         H     1  TRS     HAE     3    0.041   1.0080
    10         H     1  TRS     HAF     3    0.042   1.0080
    11         H     1  TRS     HAD     3    0.041   1.0080
    12       CH2     1  TRS      C2     4    0.090  14.0270
    13        OA     1  TRS      O2     4   -0.165  15.9994
    14        H      1  TRS     HAB     4    0.075   1.0080
....................


But Now, That is, today,  I get the output *as the following file2.itp* from
your PRODRG server for TRS ligand.
*file2.itp*
.....
[ moleculetype ]
; Name nrexcl
TRS      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1        OA     1  TRS      O1     1   -0.173  15.9994
     2         H     1  TRS     H13     1    0.061   1.0080
     3       CH2     1  TRS      C1     1    0.165  14.0270
     4      CCL4     1  TRS       C     1    0.177  12.0110
     5       CH2     1  TRS      C3     1    0.165  14.0270
     6        OA     1  TRS      O3     1   -0.174  15.9994
     7         H     1  TRS     H33     1    0.062   1.0080
     8        NL     1  TRS       N     1    0.675  14.0067
     9         H     1  TRS      H2     1    0.014   1.0080
    10         H     1  TRS      H3     1    0.014   1.0080
    11         H     1  TRS      H1     1    0.014   1.0080
    12       CH2     1  TRS      C2     2    0.144  14.0270
    13        OA     1  TRS      O2     2   -0.198  15.9994
    14         H     1  TRS     H23     2    0.054   1.0080
....

Now, I think PRODRG calculate incorrectly  cgnr   charge

What should I do? can you help me?

-- 
Ahmet YILDIRIM
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