[gmx-users] posre.itp

[Christopher Tran]

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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