[gmx-users] how to use mix solvent in gromacs

feng chen fch6699 at yahoo.com
Fri Jun 24 17:45:04 CEST 2005


  I'm a new user for gromacs.Recently I want to use
gromacs program to study a protein in a solvent of the
mixture of urea and h2o. I've noticed that there's a
file called urea+h2o.gro included in the distribution,
which means we can use the mix of urea and h2o as a
solvent without any further work. But the problem is
when I tried to the do energy minimisationby using
command like:

grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr

The system always gives me errors like:

WARNING 2 [file "topol.top", line 8269]:
  atom C1 (Res UREA-130) has mass 0

WARNING 3 [file "topol.top", line 8269]:
  atom O2 (Res UREA-130) has mass 0

It looks like the mass for all atoms in urea are zeros
in the topol.top.
Can anybody kindly tell what I did wrong? And tell me
the detail procedures for doing simulations for mix
solvent in gromacs..

thanks in advance.


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