Re: AMBER: extracting energy from trajector?

Date: Thu, 2 Dec 2004 15:56:47 -0500 (EST)

Hi David,

I still have some problems with the MMTSB:
You told me to use like that:
"make an ensemble directory from them: -dir DIR NAME NAME.pdb.*
(where DIR and NAME are chosen by you)

recursively calculate the energy over the set e.g.:
cd DIR -set etot NAME -par
param=ff99,gb=tc,gbsa=1,cut=0,gbeps=78.5 "
When I check the, I saw that the usage is like that: [options] tag [file(s)]

I am not sure about defining the "tag". I also use this tag for so
may be my problem is caused by this "tag" thing. Can you give me some more info
about tag? I could not find anything useful in the manual on web.

Thanks again,

On Mon, 29 Nov 2004 18:39:30 +0100, David Smith wrote:

> Hi Murat,
> > Unknown Amber parameter minstep will be ignored!
> I guess you have seen my previous mail by now although if it's really
> ignored it shouldn't matter.
> > cannot open file 5565.out.log at /home6/muc176/AMBER/MMTSB/perl/
> > 146.
> My guess is that this is a permission problem. Perhaps you don't have
> permission to write in the directory where you're trying to open the log
> file.
> > Can you please help me?
> I can try. Perhaps we have gone past the point where the soultion is of
> interest to the AMBER list by now. If you still can't manage, it is
> probably best just to write to me.
> Later ...
> --
> Dr. David Smith
> Division of Organic Chemistry and Biochemistry
> Rudjer Boskovic Institute
> Bijenicka 54
> 10002 Zagreb, Croatia
> tel: +385-1-4561252
> fax: +385-1-4561118
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Biomolecular Materials Lab,
Dept. of Engr. Science and Mechanics,
The Pennsylvania State University,
University Park, PA 16802
office: (814) 863 9967
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Received on Thu Dec 02 2004 - 21:53:00 PST
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