AMBER Archive (2005)

Subject: AMBER: [FWD] water minimalization problems

From: blakrose_at_gazeta.pl
Date: Wed Jul 27 2005 - 10:46:47 CDT

--
Włochy i Paryż - przewodniki turystyczne do wyboru. Tylko z lipcowym numerem miesięcznika Auto+.
http://www.a-plus.pl

attached mail follows:

I am a chemistry student form Poland from Gdansk University. I
have just started to work with AMBER so I am quite newbie in it. I
have some questions to ask.

I am doing water minimalization of Kinase-ATP complex.

This is my minimalization input:

&cntrl
imin=1, maxcyc=20000, ncyc=5000,
scee=2.0, cut=9.0, ntb=2, ntp=2,
dielc=70,
nsnb=20,
ntpr=5,
ibelly=1,
&end
not ca
0
FIND
* * S *
* * B *
* * 3 *
* * E *
N * M *
C * M *
O * M *
SEARCH
RES 1 9999
END
END

How do I know the value of dielc?
Is there a method to count it?
What do you think about this input?

Sometimes Amber stops the calculations with an error:
"RESTARTED DUE TO LINMIN FAILURE"
Why it is happening and what can I do to do minimalization to the
20000 steps?
I found that when I do my minimalization again form the *.rst
output files I can make Amber finish my minimalization.
Is it because of the steepest descent method is better in this
very moment?
Is it a good way to do minimialization again from the *.rst files?

Thanks in advance!
Regards
Pawel Gruszczynski 

-- 
Włochy i Paryż - przewodniki turystyczne do wyboru. Tylko z lipcowym numerem miesięcznika Auto+. 
http://www.a-plus.pl

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