[gmx-users] problem in recognising the atom type

[David van der Spoel]

gurpreet singh wrote:
> Thanks Mark
> 
> You said OS is not defined in 43a1 force field, so is their any way out 
> for that or i have to use a different force field.

rename OS to OA
and read the papers describing the force field (could be the gromos96 
manual in this case)

> Actually i tried using the OPLS force field but in that case i was 
> getting the similar error but this time at the CH3 atom.
> ie 'CH3 atom not found'
> Which is the better force filed for these types of simulation involving 
> these organic compunds ?
> 
> Thanks & Regards
> Gurpreet
> On 8/23/07, *Mark Abraham* <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 
>     gurpreet singh wrote:
>      > Hello Users
>      >
>      > I am using gromacs 3.3 with the force field 43a1.
>      >
>      > I have an organic compund in my simulation so i used the Dundee
>     Prodrg2
>      > server for getting the .itp file. Then i added the corresponding
>     .itp
>      > file in the top file .
>      > While running the grompp i am getting the following error
>      > Fatal error:
>      > Atomtype 'OS' not found!
>      > OS is one of the atom type in the .itp file generated above.  i have
>      > checked in the manual this is a well  defined atom type so what else
>      > could be the reason for this problem.
> 
>     OS is not defined in 43a1.
> 
>     Mark
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se