VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Sat Feb 01 2014 - 20:00:03 CST

I just noticed an error in my previous email. You should change "A" to "L" for the linear angle (NOT "LB").

Sorry for any confusion,
Christopher Mayne

On Feb 1, 2014, at 7:02 PM, Mayne, Christopher G wrote:

> Tim,
>
> I ran across this issue with a ligand I was parameterizing some time ago. Although I think I found a solution, I became distracted with something else more and never full tested the solution. If I recall correctly, you will need to make a few modifications to the hess.gau input file. You will need to find the linear angle and change it from "A" to "LB". This should tell Gaussian to treat it as a "linear bend" instead of an angle. You will also have to remove the dihedral terms that cover that angle, as linear dihedrals are undefined as far as Gaussian is concerned.
>
> If this solves the problem, please let me know and I'll update the code accordingly. If it doesn't solve the problem, let me know and I'll revisit my files to work it out.
>
> Regards,
> Christopher Mayne
>
>
>
> On Jan 31, 2014, at 8:11 PM, Tim Lo wrote:
>
>> I have a question about the parametrization of molecules involving a C-C triple bond. Take 1,2-diphenylethyne (ph-C-triple-C-ph) as an example. When I use FFTK to parametrize it, the Gaussian job of Hessian calculation (hess.gau) cannot be performed properly. From the error message in the Gaussian output file, I think, at least for the default hess.gau, Gaussian cannot deal with molecules involving a linear moiety. If so, how can I parametrize a molecule involving a C-C triple bond, esp. the angle energy terms?
>>
>> The CGenFF parameter file has 2-butyne as an example of C-C triple bond. There are indeed some angle energy terms including the sp-C (CG1T1) atom. Actually, how does one get these terms? There must be some ways to parametrize this kind of molecules but I cannot figure it out. Can anyone help? Thank you.
>>
>> Regards,
>> Tim
>
>