I have a three questions. But the most I want to get answer
is '1' !
1. Gibbs in Amber6
I have just started to use Gibbs module. But I can not understand
what I should do, even after I read the mannual. What I want to
do with Gibbs is, to calclate a free energy during changing from one
compound to
another compound. (ex, ALA to GLU or, XXX to YYY)
May be using edit command in xleap will be o.k. , but I can not to
select the first
moleclue and second moleclue which are to be pertubated. I am
confusing completely.
I can build some unique moleclues, and do MD. But I can not to use
Gibbs and interface yet.
If there are anyone who know this. please teach me or
send me some examples.
2. PARM98
In the amber6 mannual, default force filed is set to parm94.
How can I use parm98?
I think a following commnad makes good.
> prm98= loadAmberParam parm98.dat
But I am not sure. I heard from some one that parm96 is better
than parm94. So, I want to use parm96 or parm98 or parm99.
If there are anyone who know this. please teach me .
3.Monte Carlo
I have been succeeded in making Monte Carlo progarm based on
Sander_classic. But if I can choose ibelly option, I can not get
the total potential energy, only I can get is difference of potential
energy. My system is very huge one, so I want to choose ibelly option.
Even if MD simulation, once ibelly option is selected, other part of
bond energy or angle energy or dihedral energy are neglected. How can
I get the total potential energy?
If there are anyone who know this. please teach me .
///////////////////////////////////////////////////////
Thank you for reading my question.
Yu Kaneko
Ph D student of Nagoya University.
Received on Fri Mar 09 2001 - 06:33:17 PST
