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
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