AMBER Archive (2009)

Subject: [AMBER] PARMCAL calculation ?

From: Marek Maly (marek.maly_at_ujep.cz)
Date: Wed May 27 2009 - 09:19:48 CDT

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 

-- 
Tato zpráva byla vytvořena převratným poštovním klientem Opery:  
http://www.opera.com/mail/

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber