AMBER Archive (2004)

Subject: Re: AMBER: extracting energy from trajector?

From: MURAT CETINKAYA (cetinkayam_at_psu.edu)
Date: Mon Nov 29 2004 - 11:20:12 CST

Hi David,

I still could not do step3 (this time i defined the environment parameters for
MMTSB)
I cannot use eneramber.pl in the same command line with ensrun.pl
I get the following message when I try:

Unknown Amber parameter minstep will be ignored!
cannot open file 5565.out.log at /home6/muc176/AMBER/MMTSB/perl/GenUtil.pm line
146.

Can you please help me?

thanks alot
MC

On Mon, 29 Nov 2004 13:37:41 +0100, David Smith wrote:

> 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
> > >
> > > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber_at_scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > >
> > >
> >
> > 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
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> --
> 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
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>

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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