AMBER Archive (2007)

Subject: AMBER: PBSA generate snapshots

From: saccenti_at_cerm.unifi.it
Date: Thu Oct 04 2007 - 04:17:04 CDT

Dear all,
I'm trying to use the PBSA module to evaluate
the free energy of my complex.
My complex is formed by two proteins A & B and a metal ion "i" that is bonded
to both A & B.

I successfully minimized my complex A+i+B in water, and then I run a 500ps MD
getting the .mdcrd output file.

At this point I'm following the PBSA tutorial and trying to generate
snapshots but I'm a bit confused on the following points:

In my case I have (I think) a complex formed by three "molecules":
the protein A & B and the metal ion "i".

But, as the ion is coordinated to both A & B what consider LIGAND and what
consider RECEPTOR?

In the @MKCRD section I find: (pasted from the tutorial)

NUMBER_LIG_GROUPS 1
LSTART 2622
LSTOP 3862
NUMBER_REC_GROUPS 2
RSTART 1
RSTOP 2621
RSTART 3863
RSTOP 3907

So I think that I must consider two objects as RECEPTOR and one as LIGAND
(It seems reasonable to me to consider the two proteins as RECEPTOR and
the ion as LIGAND).

It is that make sense?

One more question:

COMPT ../ras_raf_II_wt.prmtop
RECPT ../ras_II_wt.prmtop
LIGPT ../raf_wt.prmtop

In my case, how to specify topology files? I mean, I have prmtop for the
A+1+B complex, must I get prmtop files for A+B and for "i" separately?

Many thanks for reading this long mail

Any help will be really appreciated!

Greets
Edoardo 

-- 
Dr Edoardo Saccenti
CERM Magnetic Resonance Center
University of Florence
Fiorgen Foundation
Via Luigi Sacconi n° 6
50019 Sesto Fiorentino
(FI) Italy
Tel: +39 055 4574281

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