AMBER Archive (2004)

Subject: AMBER: Using gibbs to calculate free energy

From: Xioling Chuang (xioling_c_at_hotmail.com)
Date: Fri Jun 18 2004 - 08:15:31 CDT

Dear amber users,

I have read tutorial concerning use of gibbs to perform free energy of 2
states; Valine to Alanine, at

http://web.njit.edu/all_topics/Prog_Lang_Docs/html/amber7/gibbs_box/val-to-ala.html#xleap_done

This is free energy between 2 different molecules. However, I would like to
calculate the free energy of dimer with 2 conformations in explicit solvent;
(I). state 0 := monomer1 is on top of monomer2 as parallel conformation
(II). state 1 := monomer1 is on top of monomer2, but twist angle between 2
monomers is 180 degree (antiparallel conformation)

As I understand, I should do as following
1). Load pdb file of state 0 to xleap
2). Edit state 0 and perturb. Since both monomers are identical, thus
PERT.name, PERT.type and PERT.charge should be the same as unperturb state.
Am I right? If yes, topology files of unperturb and perturb states should be
the same.
3). Minimization and dynamics the unperturb system to equilibrate solvent.
4). Run GIBBS
To run gibbs, I have to use restrt file from step (3) and topology file of
perturb state which is the same as unperturb state. Because pdb file of
antiparallel conformation has never used, how can I specify the different
between these two states in GIBBS?

Many thanks in advance.

Sincerely Yours,
Xioling

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