Hi All,
I am trying to slowly relax DNA-ligand complexes in a minimisation run before a md process. After making the DNA strand and inserting the ligand into the DNA I would like to hold the ligand and relax the DNA over several steps and then relax the ligand in the same manner. I am starting with a force constant of 500 down to 0 using several input files. the issue is that the ligand does not seem to be restrained right from the first step, is there another way the GROUP input should be written?
The typical input file looks like this:
............................................................
# general minimization
&cntrl
imin = 1,
maxcyc = 1000, ncyc = 5000,
ntc = 2, tol = 0.00001,
cut = 10.0,
ntpr = 500,
ntb = 1,
ntr = 1,
&end
Restrain DNA residues
500.0
RES 1 12
END
Hold ligand residues
500.0
RES 13
END
END
............................................................
Thankyou,
Andre
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Received on Sun Feb 13 2011 - 12:30:02 PST
