[gmx-users] simulation in acetonitrile

[Anton Feenstra]

srana at chem.iitb.ac.in wrote:

> 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.

The 'D1' probably is a 'Dummy' atom, which should indeed by present as an
atom type, for grompp to work. Can you show the topology file you use?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
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