VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Fri Sep 25 2020 - 17:37:45 CDT

That’s a fair point about Fe having been more common before. But with increasing interest in drug-like molecules, I would say F will come up more and more. BaseMolecule.C already has exceptions to catch two-letter elements like Na, Mg, and Cl, so I just proposed adding one for Fe as well, and then setting F to its proper value.

Of course, nothing can fully replace an engaged user like Daniel, but we can at least take away one stumbling block. Now an error will come if someone has an Fe that was truncated to F in their input, but at least VMD can’t be blamed for not reading their mind (although many try to do it anyway!). :)

Best,
JC

> On Sep 25, 2020, at 6:29 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> 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 <mailto: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 <mailto: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 <mailto: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 <mailto: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
>>>
>>
>> <5F-MDMB-PICA-frag.mol2><5F-MDMB-PICA-frag.str>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com> http://goo.gl/1wk0 <http://goo.gl/1wk0>
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.