[gmx-users] H2 topology

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 3 09:30:21 CET 2010

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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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