Dear Amber users,
I am currently trying to set up a system containing benzene with a massless dummy atom at its geometric centre. So far I have tried creating a mol2 file containing benzene and the dummy atom, with the dummy atom type defined as DU. In the mol2 the dummy atom is bound to each of the 6 carbon atoms, such that it has 6 single bonds in total. I have then built the system in leap using a frcmod file generated by prmchk. However, when I try to run a simulation, the benzene molecules become very distorted and the temperature of the system heats to ~30,000 K (I am trying to run at 300 K). I suppose that the problem is my parameters for my dummy atom are wrong. Below is the frcmod that I am currently using:
MASS
DU 0.000 0.000
BOND
ca-DU 500.00 1.400
ANGLE
ca-ca-DU 0.000 0.000
ca-DU-ca 0.000 0.000
ha-ca-DU 0.000 0.000
DIHE
ca-ca-DU-ca 1 0.000 0.000 0.000
ca-DU-ca-ha 1 0.000 0.000 0.000
IMPROPER
ca-ca-ca-ha 1.1 180.0 2.0
ca-ca-ca-DU 0.000 0.000 0.000
NONBON
DU 0.0000 0.0000 0.000
I suppose that I need non-zero parameters for the angle and dihedrals to the dummy atom, but I have no idea what would be reasonable. Does anyone who has any experience with dummy atoms have any suggestions as to how I might solve this problem?
Many thanks,
Sam Walpole, PhD Student
CAP 01.06
School of Pharmacy
University of East Anglia
Norwich Research Park
NR4 7TJ
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Received on Thu Oct 20 2016 - 08:00:05 PDT
