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From: Angela Liu <angela_ambermail.yahoo.com>

Date: Sun, 11 Sep 2005 17:43:41 -0700 (PDT)

Dear Amber developers and users,

I am learning how to use sander to carry out free

energy perturbation calculations and here are my three

questions:

1) In the older version of Amber (such as Amber 7 and

Amber 6), "gibbs" was the routine that is used to

calculate free energy perturbations. It uses "dual

topology" so that the unperturbed and perturbed

systems can have unique atoms to themselves. Kollman

indicated in his 1993 Chem Rev review that dual

topology methods often suffer from poor convergence

problems. Is this the reason why this "dual topology"

approach was no longer supported in Amber?

So if I DO want to calculate the free energy of a

mutation, say from purine to pyrimidine (a problem

clearly explained in Kollman's 1993 review with

"single topology"), is there no way Amber 8 can allow

this to be done?

2) As Pearlman and Kollman pointed out in "The

overlooked bond stretching contribution in free energy

perturbation calculations", J. Chem. Phys. 1991,

94:4532, for certain systems, bond stretching terms

are important to consider when calculating the free

energy. So in "gibbs", was the Hamiltonian expressed

according to intermediate bond stretching force

constant and equilibrium length (according to lambda

values), such as in

U_bond = [ (1-lambda) K_A + lambda K_B ] { R_AB - [

(1-lambda) R_A + lambda R_B ] }^2

where K_A, K_B, R_A, and R_B are the force field

parameters for the reactant A and product B?

Were the bond angles and torsional angles expressed

using similar equations, so that their contributions

to the free energy can be accounted for in "gibbs"?

*>From the documentation of the source files in
*

$AMBERHOME/src/gibbs/, it seems to me that these are

implemented.

3) How can I get hold of the source code of "gibbs" in

Amber 7 or 6? I tried "make" in the

$AMBERHOME/src/gibbs/ directory, but there were

problems with the Ewald routine (RE erfcfun) that

caused the "make" to fail. I wasn't sure how this can

be corrected.

Thank you very much for your time, suggestions, and

help!

Best wishes,

Angela Liu

__________________________________________________

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-----------------------------------------------------------------------

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Received on Mon Sep 12 2005 - 01:53:00 PDT

Date: Sun, 11 Sep 2005 17:43:41 -0700 (PDT)

Dear Amber developers and users,

I am learning how to use sander to carry out free

energy perturbation calculations and here are my three

questions:

1) In the older version of Amber (such as Amber 7 and

Amber 6), "gibbs" was the routine that is used to

calculate free energy perturbations. It uses "dual

topology" so that the unperturbed and perturbed

systems can have unique atoms to themselves. Kollman

indicated in his 1993 Chem Rev review that dual

topology methods often suffer from poor convergence

problems. Is this the reason why this "dual topology"

approach was no longer supported in Amber?

So if I DO want to calculate the free energy of a

mutation, say from purine to pyrimidine (a problem

clearly explained in Kollman's 1993 review with

"single topology"), is there no way Amber 8 can allow

this to be done?

2) As Pearlman and Kollman pointed out in "The

overlooked bond stretching contribution in free energy

perturbation calculations", J. Chem. Phys. 1991,

94:4532, for certain systems, bond stretching terms

are important to consider when calculating the free

energy. So in "gibbs", was the Hamiltonian expressed

according to intermediate bond stretching force

constant and equilibrium length (according to lambda

values), such as in

U_bond = [ (1-lambda) K_A + lambda K_B ] { R_AB - [

(1-lambda) R_A + lambda R_B ] }^2

where K_A, K_B, R_A, and R_B are the force field

parameters for the reactant A and product B?

Were the bond angles and torsional angles expressed

using similar equations, so that their contributions

to the free energy can be accounted for in "gibbs"?

$AMBERHOME/src/gibbs/, it seems to me that these are

implemented.

3) How can I get hold of the source code of "gibbs" in

Amber 7 or 6? I tried "make" in the

$AMBERHOME/src/gibbs/ directory, but there were

problems with the Ewald routine (RE erfcfun) that

caused the "make" to fail. I wasn't sure how this can

be corrected.

Thank you very much for your time, suggestions, and

help!

Best wishes,

Angela Liu

__________________________________________________

Do You Yahoo!?

Tired of spam? Yahoo! Mail has the best spam protection around

http://www.rosswalker.co.uk/adsense_alternatives/

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Mon Sep 12 2005 - 01:53:00 PDT

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