[gmx-users] pdb2gmx calls segmentation fault with -ff oplsaa and -dummy aromatics

Ghermes Chilov Ghermes at belozersky.msu.ru
Thu May 20 11:55:41 CEST 2004

>> 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!?

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)

 so I wondered: was it pairs cleaning process which called error? or
 something else?

any constructive solutions?!

Ghermes Chilov

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