AMBER Archive (2005)

Subject: Re: AMBER: force constant Unit used in TMD

From: Asim Okur (aokur_at_ic.sunysb.edu)
Date: Mon Apr 04 2005 - 12:36:08 CDT

Hi,

I believe the 1st paper mentioned using Targeted MD in AMBER is the
following one,

Okur A, Strockbine B, Hornak V, Simmerling C
Using PC clusters to evaluate the transferability of molecular mechanics
force fields for proteins
JOURNAL OF COMPUTATIONAL CHEMISTRY 24 (1): 21-31 JAN 15 2003

Cheers,

Asim
Viktor Hornak wrote:

>
> If you need a paper that describes TMD method implemented in AMBER7
> (and 8), here is the original reference (it's slightly different from
> original TMD method proposed by Schlitter):
>
> Apostolakis J., Ferrara P, Caflisch A: Calculation of conformational
> transitions and barriers in solvated systems: Application to the
> alanine dipeptide in water.
> J. Chem. Phys. 110(4), p. 2099 (1999)
>
> If you're looking for papers that used AMBER implementation of TMD,
> I've seen a few but don't have specific references handy...
>
> Cheers,
> -Viktor
>
> xhu1_at_memphis.edu wrote:
>
>> Thank you very much, Dr. Simmerling! Have you any suggestion about
>> reference of TMD using in AMBER? I can't find it in the manual.
>> ThankS again.
>> Regards
>>
>> Shawn
>>
>> ----- Original Message -----
>> From: Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu>
>> Date: Monday, April 4, 2005 11:06 am
>> Subject: Re: AMBER: force constant Unit used in TMD
>>
>>
>>> the energies reported by Amber are in units of per mole.
>>> Nothing is per molecule. This goes for the force constants as well.
>>>
>>> ===================================================================
>>> Carlos L. Simmerling, Ph.D.
>>> Associate Professor Phone: (631) 632-1336
>>> Center for Structural Biology Fax: (631) 632-1555
>>> Stony Brook University Web:
>>> http://comp.chem.sunysb.edu/carlosStony Brook, NY 11794-5115 E-
>>> mail: carlos.simmerling_at_stonybrook.edu
>>> ===================================================================
>>>
>>>
>>>
>>>
>>> xhu1_at_memphis.edu wrote:
>>>
>>>
>>>> Dear Amber users,
>>>>
>>>> I have a question about Targeted MD: what's the unit of force
>>>
>>> constant
>>>
>>>> used in TMD, kcal/(molecule*A^2) or kcal/(mole*A^2)? according to
>>>
>>> the
>>>
>>>> energy term: E=0.5* TGTMDFRC * NATTGTRMS * (RMSD-TGTRMSD)**2, it
>>>> should be kcal/(molecule*A^2). Am I right? Sorry for this simple
>>>> question. Thank you very much!
>>>>
>>>> Best
>>>>
>>>> Shawn
>>>>
>>>> ------------------------------------------------------------------
>>>>
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>>>
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>>
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>
> 

-- 
Asim Okur
Stony Brook University
Chemistry Department
Stony Brook, NY 11794-3400
631 - 632 1560

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