[gmx-users] Energy minimization of an UNKNOWN molecule.

[Kalyanashis Jana]

Thank you so much... I have tried to run the grompp step according to you.
But it is showing
"Fatal error:
Syntax error - File A-T.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes"
I have attached the .itp file and .top file.
Please kindly tell me, what to do now..

On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia <rosas.victor at gmail.com>
wrote:

> just put the itp file in your working directory, and include it in the
> top file of your system, so that Gromacs can find it.
>
> Hope this helps.
>
> Victor
>
> 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana <kalyan.chem.in at gmail.com>:
> > Dear all,
> > I am trying to run a gromacs simulation using an .itp file of an unknown
> > molecule ( non protein and DNA). I don't want to put the .itp file in a
> > forcefield folder and I would like put it in my working directory. Can
> you
> > please tell me, what is procedure to finish the energy minimization?
> Please
> > help me..
> > Thanks in advance,
> > Kalyanashis
> >
> > --
> > Kalyanashis Jana
> > email: kalyan.chem.in at gmail.com
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-- 
Kalyanashis Jana
email: kalyan.chem.in at gmail.com