From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Apr 01 2013 - 22:51:27 CDT

Can you make all your files available somewhere off-list? Including the fftk logs. I wrote the bonded optimization code, so I need to be aware of weird cases like this.

On Apr 1, 2013, at 11:11 PM, Win Liu wrote:

> 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
> ...
> BONDS
> !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
>
> ANGLES
> !
> !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
>
> DIHEDRALS
> !
> !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 alpha.
>
> Sorry for long email but just to clarify my problem. Thank you in advance!
> Wenhao