AMBER Archive (2002)

Subject: Summary: make_crd_hp, mm_pbsa

From: Jianhui Wu (wujih_at_BRI.NRC.CA)
Date: Mon Jul 22 2002 - 16:45:32 CDT

Dear Amber users,

I would like to thanks Dr Holger Gohlke and Samantha Hughes for their
help. It turns out that I should clean the incomplete coordinate in the
end of the first trajectory before I run mm_pbsa script. My job stopped
due to machine crashed and I restarted the job again, so there is an
incomplete set of coordinate in the first trajectory file. Secondly, I
found that I have to delete the title of the second trajectory file.
Another way to get around this is to combine the trajectory files using
ptraj.

Best regards,

Jian Hui

> I reproduced the following error for two proteins in both sgi and
> linux system. It seems 'make_crd_hg' (called by mm_pbsa script) can
> not correctly handle MD trajectory from restarted MD run (using GB
> model).
>