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.
Thank you,
Jyotsna
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
