[gmx-users] pdb2gmx-ff oplsaa and -dummy aromatics

[David]

On Thu, 2004-05-20 at 11:55, Ghermes Chilov wrote:
> >> Can I turn off generation of [ pairs ] by pdb2gmx? (OPLS topology
> >> with RB-dihedrals must not have this section, wright?!)
> D> Yes, OPLS does need the (scaled) interactions.
> 
> 
> I wondered HOW can I turn off this option while running pdb2gmx!?
you can not...

> 
> the problem - structure I have successfully manipulated with in
> GROMOS, calls segmentation fault while running pdb2gmx after line:
> ...
> Before cleaning: N pairs
> 
>  interstingly:
> 
>  a) that one chain of the protein is being processed
>  successfully, but another fails. Even two halfes of the cleaved
>  'unlucky' chain are being processed, but combined together - invoke
>  segmentation fault.
> 
>  b) fault happens only with option -dummy aromatics (without dummies
>  everything works)
....
dummy aromatics should not be used with OPLS!

> 
>  so I wondered: was it pairs cleaning process which called error? or
>  something else?
> 
> any constructive solutions?!
> 
> Ghermes Chilov
> 
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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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