VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Mon May 21 2018 - 09:45:36 CDT

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

João

On Sat, May 19, 2018 at 9:32 PM McGuire, Kelly <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>
> *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/
> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcgenff.paramchem.org%2F&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Ce44d24992d2a4d50fda608d5bdbdadb1%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636623544747133430&sdata=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*
>
> 

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851