RE: AMBER: how to use independently

From: Chris Moth <>
Date: Tue, 13 Apr 2004 10:34:26 -0500

>===== Original Message From "Jufang Shan" <> =====
>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 I am using Amber 7.

First, I have only used It calls
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

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

I found it easier to do energy outputs of the three pieces (lig, rec, lig+rec)
separately and closely check results.

In the current 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
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. 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.

Grad Student

>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

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Received on Tue Apr 13 2004 - 16:53:00 PDT
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