[gmx-users] if PRODRG calculate incorrectly

[Justin A. Lemkul]

ahmet yıldırım wrote:
> 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
> 

I agree with Tsjerk that you should contact the PRODRG developers regarding the 
differences, but I would also say that neither of these files is correct. 
PRODRG has never given reliable charges.  See, for instance (something I posted 
dozens of times before):

http://pubs.acs.org/doi/abs/10.1021/ci100335w

-Justin

> What should I do? can you help me?
> 
> -- 
> Ahmet YILDIRIM
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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