[gmx-users] posre.itp

[Christopher Tran]

Quoting Sichun Yang <syang at physics.ucsd.edu>:

> 
> Thank you for the explanation.
> But I still have some  questions.
> 
> First, how can I make sure that I used this pdb2gmx-generated posre.itp in
> the
> simualtion? I checked *.tpr and I can't tell.
> 
> Second, should I use "define = -DPOSRE" explicitly in the *.mdp file or
> should I
> put it into
> the share libarry or should I put it in the same directory with the *.top
> file which will be called by grompp?
> 

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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