|
|||||||||||||||||||||||||||||||||
AMBER Archive (2009)Subject: Re: [AMBER] i-APBS and apbs
From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Dear Dr. Robert and Jason,
Thanks for your reply! Here, I cannot say too much, may be I made some mistake. But the mainly problem is that I really want to use i-APBS in the "mmpbs.in" from the new script. In the new script, how can I explicitly set up the gid-box?
When I used APBS, the final values is -9.259764699222E+00 kJ/mol, while when I used the new script the values is - 0.5 kal/mol (indi=4, exdi=78.5) and 68kal/mol (all parameters are default) respectively! When I used apbs, the values, are usually influenced by the dimension of the grid-box and the internal dielectric. So, here I assumed the values calculated in the scipt may not be converged unless the grid-box is big enough. As a user, I admit my assumption is crude.
I have attached all my file to this email.
Rilei Yu
--- 09年11月25日,周三, Robert Konecny <rok_at_ucsd.edu> 写道:
发件人: Robert Konecny <rok_at_ucsd.edu>
Hi Rilei,
the results of APBS and sander.APBS (electrostatic or solvation energies
You can explicitly set grid size using cglen and fglen parameters while
Good luck,
Robert
On Wed, Nov 25, 2009 at 01:14:18PM +0800, Rilei Yu wrote:
_______________________________________________
_______________________________________________
| |||||||||||||||||||||||||||||||||
|