Dear Sir,
I am very sorry for this delay reply.
Thank You very much for your kind information about Antechamber in CCA-Phe terminal.
I am trying to perform MD simulation of a ribosomal part. For this I take a spherical model with 21Ǻ radius. Now I want to harmonically restrain the atoms of ribosomal part (not water or counter ions) in the region between 18Ǻ to 21Ǻ from the center with 100-kcal/mol.Ǻ2 force constant during minimization, equilibration and production run. For this, what can I write in the corresponding .in input file?
By the way during benchmark calculation I follow Amber Tutorial and for restrain purpose use the following .in input file during minimization-
&cntrl
imin=1,
maxcyc=1000,
ncyc=500,
ntb=1,
ntr=1,
cut=10.0
/
Hold the DNA fixed
500.0
RES 1 20
END
END
In this case all the residues of DNA (1 to 20) are harmonically restrained with force constant 500-kcal/mol.Ǻ2. But I want to restrain only the atoms of ribosomal part which are in the region between 18Ǻ to 21Ǻ.
I hope that I can express my problem. Have a nice Day.
Yours faithfully,
Sudarshan.
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Received on Wed Sep 07 2011 - 01:00:03 PDT
