[gmx-users] hydrogen simulation and topology file

[David van der Spoel]

vips g wrote:
> Sir thanx for the reply,
>      I have a hydrogen.pdb file which I have generated from chem sketch.
> 
> HETATM 1 H1 HYD 1 -0.353 -0.022  -0.013 1.00 0.00 H
> HETATM 2 H2 HYD 1  0.353   0.022   0.013 1.00 0.00 H
> CONECT 1 2
> CONECT 2 1
> END
> I am using genboc -ci option to insert 100 hydrogen molecules in the 
> solvated box containing water and protein.
> Now the topology file "hydrogen.itp" I am using definig hydrogen as a 3 
> point molecule.
> /
> 
> [ moleculetype ]
> ; molname nrexcl
> HYD 2
> [ atoms ]
> ; nr   type             resnr          residue             atom        
> cgnr      charge         mass
> #ifdef _FF_OPLS
>     1 opls_966           1            HYD                 
> H1                1        0.475
>     2 opls_967           1           HYD                 
> H2                1         0.475
>    3 opls_968           1           HYD                 
> DH                1        -0.950
> #endif
> 
> [dummies2]
> ;Dummy from from funct  a
>      3          1      2        1   0.5
> 
> I am confused if the pdb should also contain the dummy atom.
> Kindly give me a example as the theory in manual is little bit compact
> 
> Thanking you
> Vipul
> 
>    
> 
> /
> 
> [ moleculetype ]
> ; molname nrexcl
> HYD 2
> [ atoms ]
> ; nr   type             resnr          residue             atom        
> cgnr      charge         mass
> #ifdef _FF_OPLS
>     1 opls_966           1            HYD                 
> H1                1        0.475
>     2 opls_967           1           HYD                 
> H2                1         0.475
>    3 opls_968           1           HYD                 
> DH                1        -0.950
> #endif
> 
> [dummies2]
> ;Dummy from from funct  a
>      3          1      2        1   0.5
> 
> I am confused if the pdb should also contain the dummy atom.
yes.

just copy the coordinates from one of the atoms for your input file.
> Kindly give me a example as the theory in manual is little bit compact
> 
> Thanking you
> Vipul
> 
>    
> 
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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