AMBER Archive (2009)

Subject: Re: [AMBER] problem with FAD in tleap

From: case (case_at_biomaps.rutgers.edu)
Date: Mon Nov 30 2009 - 11:15:19 CST

On Mon, Nov 30, 2009, M. Shahid wrote:

> then tleap went find and got no complaints

Good.

> but at the end converting topology to pdb by ambpdb was not working.
>
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line
> Source
> ambpdb 0804FBA4 Unknown Unknown Unknown
> ambpdb 0804A1C5 Unknown Unknown Unknown
> ambpdb 08048222 Unknown Unknown Unknown
> ambpdb 080B15A2 Unknown Unknown Unknown
> ambpdb 08048101 Unknown Unknown Unknown
>
>
> I guess I used the wrong parameters.

The fact that ambpdb failed probably has nothing to do with what parameters
you used. We would need to know if ambpdb works for other prmtop files, what
compiler and OS (and amber version) you used, and so on.

>
> I also tried to use FAD params from
> http://www.pharmacy.manchester.ac.uk/bryce/amber
> but also doesn't work in my case.

Hard to be of much help without more information. Just saying "doesn't work"
is of no help when trying to debug something remotely.

...dac

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