From: Markus Dahlgren (markus.dahlgren_at_yale.edu)
Date: Thu May 02 2013 - 09:16:36 CDT
There is an OPLS parameter file that Dan Price prepared using the
program PEPZ that is output in the CHARMM format. The fourier
coefficients are the OPLS coefficients divided by 2. So a V1 of -5 would
be -2.5.
You also have to convert sigma and epsilon for all atom types.
I have run several NAMD simulations using OPLS and I have checked
dihedral distributions generated with NAMD and compared it with MP2
dihedral profiles that parameters were fitted against and it looks
correct. OPLS and CHARMM have very similar formats. The main difference
is the absence of CMAP in OPLS.
-Markus
On 5/2/2013 9:17 AM, JC Gumbart wrote:
> I'm not so familiar with the formats of force fields other than CHARMM, but I want to convert one for OPLS to CHARMM-style for running in NAMD. The main issue I've yet to resolve though is the format of the dihedrals. Here's an example line from the original parameter file:
>
> ; ai aj ak al funct ; Amber type OPLS type Type V1 V2 V3 Comments
> 1 4 5 6 3 -0.50208 -1.50624 0.00000 2.00832 0.000 0.000 ; C3-N3-C2-C2 4031-4030-4032-4004 5000 0.000 0.000 -0.240
>
> I realize the first part is an RB format. The second part, I guess (please correct me if I'm wrong!!!), uses this functional form:
>
> V(φ) =V1(1+ cosφ)/2+V2(1−cos2φ)/2+V3(1+ cos3φ)/2+V4(1−cos4φ)/2
>
> So for the example line, the potential would be V = -0.12*(1+cos(3*phi)). But how to represent this in CHARMM??? Because it can't be JUST a phase shift, then we would have V = 0.12*(1+cos(3*phi-180)) = 0.12*(1-cos(3*phi)). In other words, there is a constant shift in the potential energy equal to V3.
>
> What simple fact am I misunderstanding here? How does one convert force constants less than zero to charmm, where they are always greater than zero?
>
> Thanks!
> JC
>
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