VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Fri Sep 25 2020 - 08:42:57 CDT

Sure.

*Daniel Fellner BSc(Hons)*
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326

On Fri, Sep 25, 2020 at 11:39 PM JC Gumbart <gumbart_at_physics.gatech.edu>
wrote:

> Can you send me files so that I can try to reproduce the error?
>
> Best,
> JC
>
> On Sep 25, 2020, at 1:54 AM, Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
> wrote:
>
> I input a .mol2 and .str file in the "Prepare Parameterization from CGenFF
> Program Output" in the BuildPar tab. I hit Analyze Input and Write PSF/PDB.
>
> The atom type is correct in the input .mol2 and .str files
>
> *Daniel Fellner BSc(Hons)*
> PhD Candidate
> School of Chemical Sciences
> University of Auckland
> Ph +64211605326
>
>
> On Fri, Sep 25, 2020 at 4:08 PM JC Gumbart <gumbart_at_physics.gatech.edu>
> wrote:
>
>> That is disturbing. How was the PSF generated?
>>
>> Best,
>> JC
>>
>> On Sep 24, 2020, at 10:22 PM, Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
>> wrote:
>>
>> Update: I double-checked the PSF file and the entry for the fluorine
>> correctly states it's FGA1, but the molar mass listed is 55.8470 (that of
>> Fe!)...
>>
>>
>> *Daniel Fellner BSc(Hons)*
>> PhD Candidate
>> School of Chemical Sciences
>> University of Auckland
>> Ph +64211605326
>>
>>
>> On Fri, Sep 25, 2020 at 1:22 PM Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
>> wrote:
>>
>>> Hi all,
>>>
>>> I've been parameterising some compounds with fluorine atoms, and I
>>> noticed that although the PDB and PSF files correctly identify the
>>> fluorines, when any gaussian inputs are generated the program converts them
>>> to Fe. It's an easy fix, just replace "Fe" with "F" in the gaussian input
>>> files, but I'm not sure why it's happening in the first place.
>>>
>>> *Daniel Fellner BSc(Hons)*
>>> PhD Candidate
>>> School of Chemical Sciences
>>> University of Auckland
>>> Ph +64211605326
>>>
>>
>>
>