VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sat May 19 2018 - 21:31:37 CDT

I see, very interesting. So, after I've done the parameterization steps, and I then use QwikMD to set up a simulation (including adding a topo and param file for the new molecule in the structure manipulation tab), how can I check to see if NAMD is actually using my new parameters and not just the parameters in the par_all36_cgenff.prm file? Thanks for the responses, you've helped a lot!

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
Sent: Saturday, May 19, 2018 2:26:15 PM
To: vmd-l_at_ks.uiuc.edu; McGuire, Kelly; Vermaas, Joshua
Subject: RE: FFTK Tutorial Charge Opt Question

You don't. CGenFF always outputs the same results depending on the input topology. FFTK changes psfs and parameters.

-Josh

On 2018-05-19 13:21:14-06:00 McGuire, Kelly wrote:

That sounds good. One question though, after using FFTK, how do I get an updated PDB with the new parameterization?

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
Sent: Saturday, May 19, 2018 12:43:41 PM
To: vmd-l_at_ks.uiuc.edu; McGuire, Kelly
Subject: RE: FFTK Tutorial Charge Opt Question
ParamChem is probably the easiest way of getting a CGenFF charges. https://cgenff.paramchem.org/a=BcnpyusV6ODrFso3yAH13dqVhG34FwInKI2nhQbJgh8%3D&reserved=0> You'd upload a pdb, and get "best estimate" charges, as well as estimates for how awful/good the parameters it returns are.

-Josh

On 2018-05-18 23:52:19-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

In the FFTK tutorial, the optimized charges for ethanol are compared to the CGENFF values in Table 1 (page 22) by atom name. Where do I find the CGENFF charges for each

atom name/type so I can compare my molecule atom charges to the CGENFF charges? Thanks!

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602