[gmx-users] Equilibrate the water around my molecule

[Lara Bunte]

Hello

I want to equilibrate the water around my (small) molecule. In the tutorials I found and in the manual is not enough information how to do that if you have an own parametrization of a molecule. 


Here is my situation:

I have a pdb file and I have a parametrization for this molecule out of a supporting information from a paper. I create a .rtp and .hdb file, changed atomtypes.atp, ffnonbonded.itp and residuetypes.dat.


In the .rtp file I called my molecule  [ ISO ] before the [ atoms ] section starts. In the residuetypes.dat file I write 


ISO Isoalloxazin
After that I did the calculation described in the tutorial of Erik Lindahl and I got no errors up to equilibrating the water around my molecule. 

In my pr.mdp file is the entry

tc-grps         = protein non-protein

I guess this is a problem because I got an error and with best thanks I got this solution from Mark Abraham:

http://lists.gromacs.org/pipermail/gmx-users/2012-March/069096.html

I read something about make_ndx and about Thermostats but I still have no idea how to go forward with this problem :-(

Please help
Thanks and greetings
Lara