VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Sep 25 2020 - 17:29:43 CDT

JC,

there are several places where the "name" of an element is not aligned with
what VMD guesses because of the conventions in PDB files and what is common
and uncommon.

F being detected as Fe is because people were more likely to have an Fe ion
in their proteins than F atoms. similar issues happen with HE being
detected as H atom and not He due to the naming convention for the
positions of H atoms in side chains, similarly CL is detected at C and not
Cl, if I remember correctly.

The only way to get the information about an element correctly into VMD is
to use a file format that sets it explicitly or set it yourself explicitly,
if it is questionable.

On Fri, Sep 25, 2020 at 5:54 PM JC Gumbart <gumbart_at_physics.gatech.edu>
wrote:

> Hi Daniel,
>
> I found the source of this error, and I’m surprised it hasn’t been noticed
> before. It’s in BaseMolecule.C, in which VMD guesses masses based on names
> when loading a molecule. F gets flagged as Fe. I will send a separate
> email to John et al. with a proposed fix.
>
> Thanks!
> JC
>
> On Sep 25, 2020, at 9:42 AM, Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
> wrote:
>
> 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
>>>>
>>>
>>>
>> <5F-MDMB-PICA-frag.mol2><5F-MDMB-PICA-frag.str>
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.