Dear All,
I want to do a simulation of CCL4 box by amber. To do this job, I
have arranged 900 CCL4 molecule in a box of dimension 30.0, 30.0, 160.0 A.
The density of that liquid is ~1.56 gm/cc. The force field parameter was
generated from general amber forcefield file (gaff.dat) and .frcmod file by
using xleap. The newly generated .prmtop and .inpcrd files were used for our
simulation. But strangely I have found, after few thousands steps, the CCL4
molecule has broken. I have checked in .prmtop file that the number of
bonds, bends, charges, masses are correct but all atoms show same radius.
please find herewith the attached .prmtop file generated for single CCL4
molecule. please suggest me, how to overcome this problem.
thanks
sudipta
Received on Wed Mar 18 2009 - 01:18:05 PDT
