[gmx-users] Regarding PDB file

[Justin A. Lemkul]

Ravi Kumar Venkatraman wrote:
> Dear All,
> 
>              To remove water of crystallization from pdb files. I 
> removed following things from pdb file.
> 
> 
> REMARK   3   SOLVENT ATOMS            : 78
> 
> .............................................................
> .............................................................
> 
> HETATM 1072  O   HOH A 199      16.684  13.594  -5.832  0.31 
> 18.51           O
> HETATM 1073  O   HOH A 200      27.534  38.059 -12.862  0.48 
> 18.19           O
> HETATM 1074  O   HOH A 201      25.892  35.973  11.563  0.46 
> 18.15           O
> HETATM 1075  O   HOH A 202      24.790  25.182  16.063  0.46 
> 17.64           O
> HETATM 1076  O   HOH A 203      12.580  21.214   5.006  0.51 
> 17.97           O
> HETATM 1077  O   HOH A 204      19.687  23.750  -4.851  0.37 
> 18.08           O
> HETATM 1078  O   HOH A 205      27.098  35.956 -12.358  0.39 
> 18.71           O
> HETATM 1079  O   HOH A 206      37.255   9.634  10.002  0.46 
> 18.39           O
> HETATM 1080  O   HOH A 207      43.755  23.843   8.038  0.38 
> 17.96           O
> CONECT   48  981
> CONECT  238  889
> CONECT  513  630
> CONECT  601  724
> CONECT  630  513
> CONECT  724  601
> CONECT  889  238
> CONECT  981   48
> 
> Is this right or I have to delete some other things also.
> 

The only lines you absolutely must remove are the coordinate entries.  REMARK 
and CONECT lines are ignored by pdb2gmx and most other Gromacs programs.

-Justin

-- 
========================================

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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