AMBER Archive (2004)

Subject: Re: Re: AMBER: about FEP

From: Xiao He (hx_at_itcc.nju.edu.cn)
Date: Tue Nov 02 2004 - 21:18:22 CST

Dear Prof.Luo ,Case and Dave
  Thanks for your reply.I want to calculate differences in complexation free energy of two ligands binding to the same
protein and mutate one ligand into another in the presence of both protein and aqueous solution to calculate
the (delta delta G) using TI method.
  I'm not sure in the commands in leap to make the correct information for the perturbation since the two ligand changes
a bit.

He Xiao

>Annette and He,
>
>Could you let us know a bit more about your systems? How large are your
>systems? Are they solvated in water?
>
>Best,
>Ray
>
>> Dear David,
>>
>> Thanks for the response!
>> Yes, the perturbation file and everything is created ok (I have run
>> the same thing using gibbs FEP and then it works i.e. free energies
>> are calculated).
>> Now I just want to try it out with TI in sander and TI in gibbs.
>>
>> This is the gibbs FEP input that I use:
>> &cntrl
>> dt=0.002,
>> ntx=7,
>> ntpr=100,
>> temp0=300,
>> ntt=5,
>> tautp=2.0,
>> ntb=2,
>> ntp=1,
>> ntc=2,
>> ntf=2,
>> nsnb=5,
>> scee=1.2,
>> scnb=2.0,
>> nstlim=2000,
>> nstmeq=1000,
>> nstmul=1000,
>> intprt=1,
>> nrun = 21,
>> almda = 1.0,
>> almdel = 0.05,
>> isldyn = -3,
>> &end
>>
>> And I would want to have a corresponding TI input (for gibbs and one
>> for sander) for comparison.
>> Thanks in advance!
>> /Annette
>>
>>
>>
>>>>> Dear Amber users,
>>>>> I want to use thermodynamic free energy calculations,
>>>>>
>>>>> I read the manual and try a system like this
>>>>>
>>>>> nstlim=1000,ntpr=100
>>>>> icfe=1,
>>>>> clambda=0.5,
>>>>> klambda=4,
>>>>> ntb=0,
>>>>> temp0 = 300.0, tautp = 1.0,
>>>>> ntf = 2, ntc = 2,
>>>>> dt = 0.002,
>>>>> ntave = 25,
>>>>>
>>>>> But it seems it does not calculate the free energy.
>>>>
>
>
>--
>====================================================
>Ray Luo, Ph.D.
>Department of Molecular Biology and Biochemistry
>University of California, Irvine, CA 92697-3900
>Office: (949)824-9528 Lab: (949)824-9562
>Fax: (949)824-8551 e-mail: rluo_at_uci.edu
>Home page: http://rayl0.bio.uci.edu/rayl/
>====================================================
>
>
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¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Xiao He
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡hx_at_itcc.nju.edu.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2004-11-03

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