[gmx-users] Equilibrate the water around my molecule

Lara Bunte lara.bunte at yahoo.de
Fri Mar 23 19:38:52 CET 2012


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:


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

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