>===== Original Message From "Jufang Shan" <jufang_shan.hotmail.com> =====
>Hi,
>
>I want to calculate the binding free energy between receptor and ligand. I
calculated the entropy for the complex, receptor and ligand using normal mode
separately since the same parameters don't work for all. My question is what
value shall I give to "calc delta" (?0..1) and "calc decomp" (?0..2) to run
mm_pbsa_statistics.pl? I am using Amber 7.
>
First, I have only used mm_pbsa.pl. It calls mm_pbsa_statistics.pl
for you and fills in these values.
If you are just calculating free energy of ligand binding, and you don't
care about residue-by-residue analysis (yet), set DC=0 in your input file to
mm_pbsa.pl.
You wil get statistical output as soon as you specify MM in your input file
(which also causes the perl script to call sander).
==========================================================================
Here are some longer notes I wrote before I reread your question :)
Perhaps they will be helpful....
Did you already create snapshots and compute MM and PB energies for ligand,
receptor and ligand+receptor without cutoffs using the MM_PBSA Perl script?
You must do this before it can proceed to the totals and statistics.
Use GC to output snapshots - but noted that ptraj is not used for this. You
must specify atom ranges for the make_crd program which is called by the
script.
I found it easier to do energy outputs of the three pieces (lig, rec, lig+rec)
separately and closely check results.
In the current mm_pbsa.pl script, the calculation of energy is tied to the
statistics output. So, it expects to do all the calculation first.
If you want to do things one step at a time... then when you have all the
energies in the .out files, Just comment out this part of the mm_pbsa.pl
script (if your system is tightly managed, copy the mm_pbsa code to your own
directory) which calls sander:
# if($GEN{"MM"} || $GEN{"NM"} || $GEN{"PB"} || $GEN{"GB"} || $GEN{"MS"}){
# Calc single energy and entropy contributions
# &calc_energy_entropy(\%GEN,\%DEC,\%DEL,\%MOL,\%PRO);
# }
In my own work, I added back entropy values to the MM, PB and surface area
numbers "by hand". This was not a big problem.
I also recommend that practice on small sets of snapshots before you go to
final processing and statistics output. mm_pbsa.pl is a great script - but
you don't want to make a mistake or get caught in a bug - and learn that only
after a lot of calculation.
Best of luck.
Chris
Grad Student
Vanderbilt...
>Thanks,
>Jufang
>
>----------------------------------------------------------------
>Jufang Shan
>Graduate Student
>Dept. of Structural Biology
>St. Jude Children's Research Hospital
>Interdisciplinary Program
>The University of Tenessee Health Science Center
Chris Moth
chris.moth.vanderbilt.edu
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Received on Tue Apr 13 2004 - 16:53:00 PDT
