Hi,
I have one protein structure where I have to change a residue and need
the same amount of water molecules for each simulation - so I solvate
one and then make a pdb file changing the residues' properties when I
do the minimization amber does not produce any output but just
"hangs". I have look into the generation of the prmtop and inpcrd
files and I do not get any error messages there. I get warnings on how
close the atoms are together. I do not know how to debug the problem
with the new prmtop/inpcrd. My minimization looks like this
Minimization of water
&cntrl
imin = 1,
maxcyc = 10000,
ncyc = 5000,
ntb = 1,
ntr = 1,
cut = 12
/
Hold protein fixed
500.0
RES 1 200
END
END
thanks in advance
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Received on Thu Jan 19 2012 - 01:30:03 PST
