AMBER Archive (2009)

Subject: Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Sat Nov 14 2009 - 11:06:15 CST

> Thanks a lot for your kind help. After doing correction of spelling when i
> again run this calculation this error removes, but the last error of
> segmentation fault appears, i am again sending you modified script after
> spelling correction. The error is
>
> Checking coordinates: 2HT0_wat_1-5.binpos
> Segmentation fault

"Segmentation fault" is not a very descriptive error message and usually
occurs when memory gets trampled or misaccessed... You could try to use
gdb to look at a more detailed error message.

unlimit coredumpsize
traj ptraj.in
 (dumps a core.* file)

gdb ptraj corefile
where

As it looks like it is failing while reading coordinates, make sure
something is not wrong with the input trajectory (was the trajectory file
moved between Unix/DOS or different machines; if so there could have
been an endian flip?).

Also note that you may want to start small; just try a simple ptraj script
first...

trajin 2HT0_wat_1-5.binpos
rms first mass out rms

Finally, I notice that this line may be trouble since it lacks 1-1 mapping
between names...

> > > acceptor mask :2-11,13-16,20_at_N :2-20_at_H

acceptor mask :2-11,13-16,20_at_N :2-11,13-16,20_at_H

--tec3

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