[gmx-users] simulation in acetonitrile

[srana at chem.iitb.ac.in]

Hi all,

I was trying to set up a simulation in acetonitrile using the MeCN box and
the MeCn.itp uploaded at www.gromacs.org provided by a gentleman.I went
through all the mails that is stored  in the site but could not solve my
problem.Hence am addressing you all for a possible solution.

After soaking the protein in aetonitrile i got the following error while
attempting for energy minimization.
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 135 of the 1081 non-bonded parameter combinations
Cleaning up temporary file gromppHhPiRE
Fatal error: Invalid order for directive atomtypes, file
""acetonitrile.itp"", line 1

Then i included the #ifndef..in the first line and #endif in the end.

in my second attempt i got the following error.
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 135 of the 1081 non-bonded parameter combinations
Cleaning up temporary file gromppPzYl49
Fatal error: Atomtype 'D1' not found!

i included the atomtype in ff///.atp but couldn,t solve the problem.

Could anyone please help me in setting up a simulation in acetonitrile or
could point out that where am wrong?

Thanking you all.

Soumendra
IIT Bombay