[gmx-users] Free volume: Pass and Gromacs

[David van der Spoel]

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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