[gmx-users] if PRODRG calculate incorrectly

[Tsjerk Wassenaar]

Hi Ahmet,

The PRODRG server is not related to Gromacs. If you encounter problems
pertaining to the server or the outcome from it, you should drop a
line to the PRODRG development team.

Cheers,

Tsjerk

2011/9/17 ahmet yıldırım <ahmedo047 at gmail.com>:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands