[gmx-users] Free volume: Pass and Gromacs

[Alessandro Mattozzi]

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

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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-- 
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://folding.bmc.uu.se
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