From: Win Liu (
Date: Mon Apr 01 2013 - 22:11:35 CDT

Hi VMD developers,
For a simple test to develop the forcefield with benzene molecule. In pdb
and psf, Since benzene only had one type of carbon and hydrogen, CA and HP
respectively. So the initial parameter file is
!V(bond) = Kb(b - b0)**2
!Kb: kcal/mole/A**2
!b0: A
!atom type Kb b0
CA HP 0.000 0.000
CA CA 0.000 0.000

!V(angle) = Ktheta(Theta - Theta0)**2
!V(Urey-Bradley) = Kub(S - S0)**2
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!atom types Ktheta Theta0 Kub S0
CA CA HP 0.000 0.000
CA CA CA 0.000 0.000

!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!atom types Kchi n delta
CA CA CA CA 0.0000 1 0.00
HP CA CA CA 0.0000 1 0.00
HP CA CA HP 0.0000 1 0.00
When I am doing the bond calculation to get bond and angle parameters, I
went through the hess calculation in Gaussian and used fftk to get
BondedCalc.log file, I found the parameter, angle {CA CA HP} 0.000 0.000
Obviously, this is not right(while bond {CA CA}, bond {CA HP}, angle {CA CA
CA} all give reasonable non-zero value.) it seems that the fftk do not get
the information for this angle.
And when I l dealt with Scan torsion module, in Dihedrals to scan table, I
can only see CA CA CA CA dihedral(like 10 0 2 4, 6 8 10 0 and so on) but no
HP CA CA CA or HP CA CA HP dihedrals, but they should be included, right?
In addition, in my fftk plugin, I can not use "Edit Entry" tab, is it the
issue that need to be fixed for VMD windows version? I am using 1.9.2

Sorry for long email but just to clarify my problem. Thank you in advance!