[gmx-users] Mixed solvents

[luigi.burgi at virgilio.it]

I have a problem in simulating a Protein (1ypc) in water + other 
solvent.
I'll have to do md for several molecules as co-solvent (co-
solute) and i have started with Taurine.
     OH
     |
O=S=O
     |
     CH2
     |
     CH2
     |
     NH2

I have made the following 
steps:

1. Used the PRODRG server to generate topology and coords for 
the small molecule
2. Made a small box of Taurine + water and made md 
with p-coupl on (everything ok)
3. editconf to make a box around 
protein
4. Solvate the protein with genbox and the newly created box as 
solvet (ok)
5. Started an energy minimization (problem)

The problem is 
that during the minimization the Taurines are exploding. It seems as 
they are not kept toghether by their .itp topology included in topol.
top

Many thanks for every help,
Luigi Burgi

CCG University of Milan