subarna thakur wrote:
Hello
We dont have the parameters for Fe4S4 cluster in any of the the gomacs force
fields but if we able to make the .itp file for the cluster manually with the
help of Quantum mechanical calculations, can we place the .itp file of fe4s4 in
the include section of the protein .top file later as done in the case of
drug/enzyme tutorial of gromacs.Can we fellow the steps given in the tutorial
for the Fe4S4 cluster?
Yes and no. Even if you are able to obtain suitable parameters (which
will be difficult at best), if there are bonded interactions to the
cluster, then you will have to make a composite topology - i.e. a single
[ moleculetype ]. Depending on the geometry and sequence order of your
two chains, that might be painful too.
Frankly, this project would be a very poor one for a first effort at MD.
Get some experience with GROMACS doing something more straightforward,
learning to walk, before trying to run juggling razors.
Mark
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