On 2/1/10 10:57 AM, 011013021-Jyotsna wrote:
Dear all,
I want to run a simulation for an enzyme. It demands me to incorporate a
Molecular hydrogen Topology with a dummy atom in between in the
simulation in order to study the path of hydrogen in it.The problem is ,
the topology file I built induces many errors when i come to the energy
minimization step. The version of gromacs I am using is 4.0. The
topology file I built is as follows
[ moleculetype ]
;name nrexcl
H2 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass ; total charge
1 H 1 H2 H1 1 0.475 1.00800 ; 0.00
2 H 1 H2 H2 1 0.475 1.00800 ; 0.00
3 DUM 1 H2 DUM 1 -0.950 0.000
[ virtual_sites2 ]
; Site from funct a
3 1 2 1 0.7439756
When ever I insert the hydrogen+dummy atom topology in the protein's
.gro file, an error is generated regarding mismatch of residues or the
dummy atom having mass 0 .
I would be really grateful if anyone could provide me the hydrogen
molecule topology and give some pointers towards it.
Please print the error message in your mail.
Topology look OK, but you need to add a bond or constraint.
Also the constant probably has to be 0.5 since you want the vsite in the
center of the two atoms.
Thank you,
Jyotsna
--
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.
[email protected] [email protected] http://folding.bmc.uu.se
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