AMBER Archive (2005)

Subject: AMBER: Tutorial question and some more...

From: blakrose_at_gazeta.pl
Date: Tue Aug 09 2005 - 01:49:45 CDT

Dear Amber Users!
 
Is it a good way to minimise a structure e.g. peptide at first in
the vacuum then add water and do steps a) minimise with ntr=1 then
b) minimise whole structure?
 
My second question is about Beginners Tutorial part 5 (Running
minimisation in explicit water). Why in the minimisation stage the
constant pressure is not on? Is it because of low temperature?
 
My third question is about something else :-)
What I can do (besides looking) when in my output minimisation
sander "battles" with one atom, and in the end it is written
"RESTARTED DUE TO LINMIN FAILURE"(all knows what it means), and I
would really like to do minimisation stage till the end.
 
Thans in advance
Regards
Pawel d;-) 

-- 
Tylko w sierpniu Avanti także w wersji MINI - z łatwością zmieści się w torebce!
http://www.avantimoda.pl
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