VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Fri Sep 25 2020 - 06:39:47 CDT

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 <mailto: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 <mailto: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 <mailto: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
>