AMBER Archive (2004)

Subject: Re: AMBER: extracting energy from trajector?

From: David Smith (David.Smith_at_irb.hr)
Date: Mon Nov 29 2004 - 06:37:41 CST

Hi Murat,

I think the key is that (if you followed the steps) you are in a
subdirectory.

Try ../enerAmber.pl ......

I guess what you are missing is the environment variable MMTSBDIR

in csh:
setenv MMTSBDIR /usr/local/chem/mmtsb (or wherever you put it)
in bash:
export MMTSBDIR=/usr/local/chem/mmtsb (ditto)

Also you may need to fix your path

in csh:
set path= ($path /usr/local/chem/mmtsb/bin) (or wherever it is)
set path= ($path /usr/local/chem/mmtsb/perl) (ditto)
in bash:
export PATH=$PATH:/usr/local/chem/mmtsb/bin:/usr/local/chem/mmtsb/perl
(ditto ditto)

Be aware that mmtsb will check your AMBERHOME environment variable so it
should point to your amber installation. Finally, you may have a problem
with the ordering of the frames. If you get that far and need to know
the original frame order, feel free to write again.

Good luck....

On Mon, 2004-11-29 at 01:59, MURAT CETINKAYA wrote:
> First of all, thanks for the tips from everybody. I tried David Smith's method
> but I got stuck in step 3 (described below).
>
> In order to run the perl files i must use "./perl_name". However, in step3 i
> must use two files at the same command line and i get the following message :
> sh: ./enerAmber.pl: No such file or directory
>
> I also could not set the home directory for MMTSB(probably i do not have the
> permission). Is there any other way to use ensrun and enerAmber separately.
>
> Hope my question is clear...
>
> Thanks in advance.
>
> On Wed, 24 Nov 2004 20:29:34 +0100, David Smith wrote:
>
> > Hi Murat,
> >
> >
> > > I need to extract the energy values of my system from my trajectory file
> created
> > > by sander. I have lost my mdout file so, I will either re-run the simulation
> > > (but i do not have time for it) or find a way to get these energy data from
> my
> > > crd file.
> >
> > Another possibility is with the MMTSB toolkit
> > (http://mmtsb.scripps.edu/)
> >
> > It is quite easy to install and quite nice to use. Apart from possibly
> > solving your current problem, you may find it quite useful for lots of
> > things. Depending on how sophisticated your md run was you may get away
> > with something like the following:
> >
> > 1) convert your trajectory to pdbs with ptraj
> > 2) make an ensemble directory from them:
> >
> > checkin.pl -dir DIR NAME NAME.pdb.*
> >
> > (where DIR and NAME are chosen by you)
> >
> > 3) 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
> >
> > (the last command should be all on one line and should be adjusted [if
> > possible] to suit your run, the web documentation is pretty good)
> >
> > and then you can get the energies by:
> >
> > getprop.pl -prop etot NAME
> >
> >
> > Anyway, it may seem a bit complicated but I have found it a very helpful
> > toolset for lots of things.
> >
> > Good luck.
> >
> >
> > --
> > 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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
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-- 
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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