I am currently experiencing problems trying to minimise just the waters of
a solvateOct that surrounds a protein. During minimisation the protein has
been restrained but consistently I get escaping atoms problems. I have
increased the closeness value to 3.5 as I thought the waters might be
being expelled due to being to close to the solute. Unfortunately this
course of action has not helped and I would be very grateful for any ideas
as to get around this problem. I am currently using AMBER 6.0 and am using
sander_classic for the minimisation. The mdin I am using is:
&cntrl
imin=1,
maxcyc=100000,
cut=8.0, scee=1.2,
ntb=1,
ntr=1,
ntpr=100,
ncyc=5000,
&end
Group atoms for restraining chym
5.0
RES 1 237
END
END
Thank you once again
Charly
Received on Wed Sep 04 2002 - 03:43:03 PDT
