[AMBER] PARMCAL calculation ?

From: Marek Maly <marek.maly.ujep.cz>
Date: Wed, 27 May 2009 15:19:48 +0100

Dear Amber users,

I have just technical question regarding PARMCAL from Amber10.

If I need to calculate bond force constant between atoms A-B, program asks
me
for element type of atom A, B and on the end for the equilibrium lenght
of the bond A-B.

Here program tells:

----------------------------------------------------
Please input the bond length (a non-positive number
means to calculate it according to empirical rules
----------------------------------------------------

similarly if i want to use PARMCAL to compute angle force constant,
program ask me:

---------------------------------------------
Please input the bond angle (a non-positive number
means to calculate it according to empirical rules
---------------------------------------------


I suppose that sentence "according to empirical rules" refers on the
generalised
method used for parametrisation of MMFF 94 which is described in detail in
the article
"Development and Testing of a General Amber Force Field".
But my question is what algorithm is used (to calculate bond/angle force
constants) if I provide
to PARMCAL POSITIVE value of the bond length/angle ?

Thanks in advance for the information !

       With best wishes

              Marek




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Received on Thu May 28 2009 - 01:09:30 PDT
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