[gmx-users] posre.itp

[Sichun Yang]

Thank you for your response.

Now I used define = -DPOSRE. But when I check the log file of grompp,
I found as follows:

 position_restraints:                 atoms               invalid

Does it mean that posre.itp isn't included yet? I also search the log
file, I can't find the posre.itp has been called? What did I miss? 
What is the 'ideal' location of  posre.itp?

Thanks,
-Sichun

> 
> I would put define = -DPOSRE into the mdp file.
> 
> If the following is found in your .top file:
> 
> #ifdef POSRE
> #include "posre.itp"
> #endif
> 
> then posre.itp will be included if you have used define = -DPOSRE in the mdp 
> file read by grompp.
> 
> > Thanks,
> > -Sichun
> >  
> > 
> > > > 
> > > Check chapter 5.
> > > 
> > > itp files must eb included in the topology, as in the C-programming
> > > language. posre.itp is generated by pdb2gmx if you process a protein
> > > with it.
> > > 
> > > > Thanks,
> > > > -Sichun 
> > > > 
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> > > -- 
> > > David.
> > > ________________________________________________________________________
> > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > > Dept. of Cell and Molecular Biology, Uppsala University.
> > > Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> > > phone:	46 18 471 4205		fax: 46 18 511 755
> > > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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