[gmx-users] pdb2gmx-ff oplsaa and -dummy aromatics
spoel at xray.bmc.uu.se
Thu May 20 14:12:25 CEST 2004
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
> 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 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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