From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Mon May 21 2018 - 12:44:05 CDT

I see. I do get those "Duplicate bonds and angles" lines in the log file, and below that it does show the values from my new parameters, but then it says using the parameters from the cgenff param file...

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: Monday, May 21, 2018 11:05:26 AM
To: jribeiro_at_ks.uiuc.edu; McGuire, Kelly
Cc: vmd-l_at_ks.uiuc.edu; Vermaas, Joshua
Subject: RE: vmd-l: Re: FFTK Tutorial Charge Opt Question

Uhh... No. Check NAMD logs when this happens. It'll say something like "DUPLICATE <bond/angle/dihedral> ENTRY FOR ...", and then give the old and new values. My reading of the NAMD source (Parameters.C) is that it will always replace a value, so your new stuff should come last in the list of parameters.

-Josh

On 2018-05-21 08:46:04-06:00 Joo Ribeiro wrote:

Hi Kelly,
I am glad you that you were able to add the new topology to QwikMD. As a rule of thumb in the generation of new topologies, one should avoid using the same atom names and types already in use in the forcefield if the new atoms are different to avoid any conflicts.
If I am not mistaken, NAMD will use the parameters defined in the first parameter files listed (they are not overwritten), which in the configuration files prepared by QwikMD will be the new stream file that you provided.
Best
Joo

On Sat, May 19, 2018 at 9:32 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:

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<mailto:Joshua.Vermaas_at_nrel.gov>>
Sent: Saturday, May 19, 2018 2:26:15 PM
To: vmd-l_at_ks.uiuc.edu<mailto: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<mailto:Joshua.Vermaas_at_nrel.gov>>
Sent: Saturday, May 19, 2018 12:43:41 PM
To: vmd-l_at_ks.uiuc.edu<mailto: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<mailto: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

--
...
Joo Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
jribeiro_at_ks.uiuc.edu<mailto:jribeiro_at_ks.uiuc.edu>
+1 (217) 3005851