[gmx-users] posre.itp

[Sichun Yang]

Please fix the typo for the define option of mdp in the manual; 
it shoud be -DPOSRES (note the final S) instead of -DPOSRE.

-Sichun

On Wed, 18 Aug 2004, Christopher Tran wrote:

> Quoting Sichun Yang <syang at physics.ucsd.edu>:
> 
> > 
> > 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
> > 
> 
> A good place for posre.itp would be in your working directory; ie the same 
> directory as all of your other files for your simulation, and the same 
> directory where you run Gromacs commands.  As posre.itp will be different for 
> different proteins, I wouldn't suggest putting it into gmx/share/top.
> 
> Christopher Tran
> 
> > > 
> > > 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
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> ~spoel
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