I have a question of Amber Tutorials-A1. Anyone can help with this question,
thank you!
http://ambermd.org/tutorials/advanced/tutorial1/
In this tutorial, it seems to me that amber uses the partial charges
computed from Gaussian.
But i don't know why these values of partial charges computed from Gaussian
become
totally different after importing to Amber.
Pls compare these two file:
1) the result from Guassian computation: Figure 1.4 at
http://ambermd.org/tutorials/advanced/tutorial1/section1.htm
2) after manual assigning the type and the partial chage to each atom and
generate the file of fam5.lib and fam5_leap.pdb in Section 3.3.1) Saving
our new library file
http://ambermd.org/tutorials/advanced/tutorial1/section3.htm
you also can use xleap to see the charges
$AMBERHOME/exe/xleap &
loadoff fam5.lib
loadamberparams fam5.frcmod
FAM = copy FAM5
mol = loadpdb fam5_leap.pdb
edit mol
you can see the charge of atoms
They are totally different from the ones shown in Figure 1.4 which are
calculated from Gaussian.
Can anyone help exlain this? thanks!
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Received on Wed Jan 27 2010 - 14:00:03 PST
