[gmx-users] HELP .....changing charges in the forcefield

[saurabh shakya]

there are total 2 irons and 2 sulfurs which are
covalently bonded as a iron sulfur cluster. these
irons in turn are bonded to 2 cystines each making a
total of 4 cystines bound to the 2 irons of the
cluster. These cystines are covalently bonded to the
Fe of the cluster  by the Sg . 
Other thing which puzzles me is that the same topology
with the default gromacs charges was running fine in
position restrained and unrestrained md run .But after
I alter the charges in the same topology ,lincs error
starts coming in position restrained md .

Regards 
Saurabh


there is not a real problem with modifying charges, I
suspect there is
still something else in the topology. How are the
cysteines connected 
to
the Iron-Sulfur cluster? How many Iron and Sulfur and
Cysteines do you
have?

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