AMBER Archive (2004)

Subject: Re: AMBER: extracting energy from trajector?

From: MURAT CETINKAYA (cetinkayam_at_psu.edu)
Date: Thu Dec 02 2004 - 14:56:47 CST

Hi David,

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

recursively calculate the energy over the set e.g.:
cd DIR
ensrun.pl -set etot NAME enerAmber.pl -par
param=ff99,gb=tc,gbsa=1,cut=0,gbeps=78.5 "
----------------------------------------------------
When I check the checkin.pl, I saw that the usage is like that:

checkin.pl [options] tag [file(s)]

I am not sure about defining the "tag". I also use this tag for enerAmber.pl 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,
Murat

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/GenUtil.pm
line
> > 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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>

Murat CETINKAYA
Biomolecular Materials Lab,
Dept. of Engr. Science and Mechanics,
The Pennsylvania State University,
University Park, PA 16802
office: (814) 863 9967
web: www.personal.psu.edu/muc176
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