[gmx-users] Free volume: Pass and Gromacs

[Erik Marklund]

On Thu, 2006-06-08 at 15:14 +0200, Alessandro Mattozzi wrote:
> Is it necessary to specify the atomtype in the index file or is it read from the .gro file or the .tpr? Because i guess some data are needed (vdW radius) to insert spheres in the free volume.
> Thanx
> 

Index files generally contain only atomic indexes and group names. As
such, they only specify sets of atoms, and there is no way of specifying
any additional information in the index file. See the manual for
slightly more information. Atomtype, name and such stuff is as far as I
know indeed read from the structure file (for example a tpr-file). The
point of making an index file in this case is, I guess, that make_ndx
creates a group consisting of the non-dummies.

Erik Marklund
Ph.D. Student
ICM, Molecular biophysics
Uppsala University
Sweden

> Alessandro Mattozzi
> M.Phil., Ph.D. student
> Dept. of Fibre and Polymer Technology
> Royal Institute of Technology
> Stockholm, Sweden
> 
> 
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
> Sent: Wed 6/7/2006 5:14 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Free volume: Pass and Gromacs
>  
> Alessandro Mattozzi wrote:
> > Hi all
> > I wonder if anybody has been using Pass to measure free volume: I got 
> > these errors:
> > 
> > -Error:  Found an odd element (B) on atom #13454.  Hydrogen radius assigned.
> > Suggestion: Do I have to remove all the dummies?
> Yes.
> 
> make an index file, it will have a suitable group for it.
> 
> > 
> > -Segmentation fault
> > Suggestion: I use trjconv to get a pdb; is it possible that I am doing 
> > some mistake in the conversion?
> > 
> > Thanx
> > 
> > Alessandro Mattozzi
> > M.Phil., Ph.D. student
> > Dept. of Fibre and Polymer Technology
> > Royal Institute of Technology
> > Stockholm, Sweden
> > 
> > 
> > ------------------------------------------------------------------------
> > 
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