## VMD-L Mailing List

**From:** Mayne, Christopher G (*cmayne2_at_illinois.edu*)

**Date:** Fri Feb 07 2014 - 17:33:11 CST

**Next message:**Tim Lo: "Re: triple bond parametrization"**Previous message:**chandrakala gowda: "Re: measure dihedral angle for all the loaded pdb files"**In reply to:**Mayne, Christopher G: "Re: triple bond parametrization"**Next in thread:**Tim Lo: "Re: triple bond parametrization"**Reply:**Tim Lo: "Re: triple bond parametrization"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Tim,

Sorry it's taken me a while to get back to this. I ran some tests on acetonitrile today. Using standard cartesian definition, the Gaussian geometry optimization proceeded without error. Then after converting the linear angle from "A" to "L" and removing the dihedrals involved in the linear angle, the hessian calculation completed without error. If the linear angle is left out, the bond and angle optimization proceeds without error. When including the C-C-N angle in the optimization, ffTK threw an error. Without having looked into it too far, I believe that this is an error in how ffTK tries to interpret the "L" entry, and I'll have to look further into it.

All of that said, it sounds like your particular error is originating from your modification of the Gaussian input file when running the initial geometry optimization, and is propagating to the hessian (ffTK tells Gaussian to pull the geometry used in the hessian calculation from the geometry optimization checkpoint file). so you may have to start over to correct the errors you're seeing. In the meantime, I'll try to fix the error associated with how ffTK reads in the "L" terms.

Regards,

Christopher Mayne

On Feb 1, 2014, at 10:44 PM, Mayne, Christopher G wrote:

*> Tim,
*

*>
*

*> Make sure to cc VMD-L on this type of email so that others can learn from our discussion.
*

*>
*

*> Yes, the internal coordinate system is crucial for bond optimization. The short reasoning is because the IC system is defined to match molecular connectivity, hence the hessian maps directly to the desired distortions for the optimization. I will have to take a closer look and revisit some test cases when I'm back in the office on Monday.
*

*>
*

*> Christopher Mayne
*

*>
*

*> On Feb 1, 2014, at 9:51 PM, Tim Lo wrote:
*

*>
*

*>> Dear Christpoher,
*

*>>
*

*>> This has partially solved the problem and Gaussian can start the calculation. But at the end, the output file says "Error in internal coordinate system." When I click the "guess" button in the "Opt. Bonded" tab, there is an error message: "Couldn't read internal coordinate table!"
*

*>>
*

*>> Actually, at the beginning of the parametrization procedure in "Opt. Geometry", I also encountered this internal coordinate system error in the Gaussian output file. I just bypassed this problem by modifying the Opt part in the input file as "Opt=(Z-matrix)" or "Opt=(Cartesian)". I think the use of internal coordinate system is problematic for linear molecules. Must the internal coordinate system be used in "Opt. Bonded"? How to solve it or bypass it?
*

*>>
*

*>> Regards,
*

*>> Tim
*

*>>
*

*>> On 2014/2/2 上午 10:00, Mayne, Christopher G wrote:
*

*>>> 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
*

*>>>>
*

*>>
*

*>
*

*>
*

**Next message:**Tim Lo: "Re: triple bond parametrization"**Previous message:**chandrakala gowda: "Re: measure dihedral angle for all the loaded pdb files"**In reply to:**Mayne, Christopher G: "Re: triple bond parametrization"**Next in thread:**Tim Lo: "Re: triple bond parametrization"**Reply:**Tim Lo: "Re: triple bond parametrization"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]