On 2/3/10 7:52 AM, 011013021-Jyotsna wrote:
Dear Justin ,
Thank you very much for your help.
To create a linear H2 molecule with a dummy atom in the center is
proving to be quite a difficult task.
Hence , I created a pdb file of CO2 using Cerius(2) , and replaced the
atoms in the pdb file with 2 H atoms and a dummy atom.(since CO2 is a
three atom , linear system i.e the two O atoms replaced by two H atoms
and the C atom by the dummy)
The problem is the bond distance. For CO2 , it is 1.66 A but I need the
distance for H2 to be only 0.7 A as per the literature I am following.
By replacing the atoms in the pdb file , there is a problem regarding
distance since the coordinates of the pdb also point towards 1.6 A.
I would be very grateful if you could tell me how I can build a PDB for
H2 with dummy atom with the right distance.
Thank You,
Jyotsna
Doesn't matter if the pdb is wrong initially, you just do an energy
minimization. What is important is (put in exact bond length):
[ bonds ]
1 2 1 0.74 500000
[ vsites2 ]
3 1 2 1 0.5
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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