VMD-L Mailing List

From: CHARLES MCCALLUM (cmccallum_at_me.com)
Date: Tue Mar 04 2025 - 11:23:32 CST

I really appreciate Josh’s willingness to help (Go State!), but I think probably I need help from an author of the ffTK tutorial from 2015. I believe the point of this tutorial is to
1) show how to parameterize a new, smallish molecule
2) use ethanol, from scratch, because the results may be compared to the established ETOH, standard parameterization.

After Josh’s reply, I re-did the tutorial, and tried a couple things.

First, I made the resname “ETO”, but that returned no coordinates. This made me realize Molefacture IS taking coordinates from the established ETOH. I then re-ran and made sure the oxygen was attached to the C1 carbon (though the OH hydrogen ended up being index 8/atom 9 in the Molefacture table), and used “ETOH”. This returned a full set of coordinates, so I guess we can move on, but I’m a bit skeptical about the rest of the workflow.

REMARK original generated coordinate pdb file
ATOM 1 C1 ETOHA 1 0.000 0.000 0.000 1.00 0.00 A C
ATOM 2 O1 ETOHA 1 -0.495 1.437 -0.000 1.00 0.00 A O
ATOM 3 HO1 ETOHA 1 -1.902 1.714 -0.000 1.00 0.00 A H
ATOM 4 H11 ETOHA 1 -0.326 -0.473 0.819 1.00 0.00 A H
ATOM 5 H12 ETOHA 1 -0.326 -0.473 -0.819 1.00 0.00 A H
ATOM 6 C2 ETOHA 1 1.500 0.000 0.000 1.00 0.00 A C
ATOM 7 H21 ETOHA 1 1.872 -0.103 1.042 1.00 0.00 A H
ATOM 8 H22 ETOHA 1 1.899 -0.852 -0.592 1.00 0.00 A H
ATOM 9 H23 ETOHA 1 1.909 0.945 -0.419 1.00 0.00 A H
END

Why does the tutorial explicitly use a different order? Somehow this worked, as the example files have a full set with this different order:

REMARK original generated coordinate pdb file
ATOM 1 C1 ETOHL 1 0.000 0.000 0.000 1.00 0.00 L C
ATOM 2 H11 ETOHL 1 -0.326 0.946 -0.000 1.00 0.00 L H
ATOM 3 H12 ETOHL 1 -0.326 -0.473 0.819 1.00 0.00 L H
ATOM 4 H13 ETOHL 1 -0.326 -0.473 -0.819 1.00 0.00 L H
ATOM 5 C2 ETOHL 1 1.500 0.000 0.000 1.00 0.00 L C
ATOM 6 H21 ETOHL 1 1.872 -0.103 1.042 1.00 0.00 L H
ATOM 7 H22 ETOHL 1 1.899 -0.852 -0.592 1.00 0.00 L H
ATOM 8 O2 ETOHL 1 2.059 1.292 -0.573 1.00 0.00 L O
ATOM 9 HO2 ETOHL 1 1.186 2.397 -0.844 1.00 0.00 L H
END

What am I missing here?

Best,
Mike

> On Mar 4, 2025, at 07:42, CHARLES MCCALLUM <cmccallum_at_me.com> wrote:
>
> Josh, thanks.
>
> However, I understand how psfgen does things, as we’ve been doing that for years. However, I’m trying to do things through Molefacture. Why isn’t following the tutorial working? The goal is toe parameterize some new molecules we want to use. If I’m trying to teach people an easier way, front to back, to parameterize new molecules, I’d like to be able to stick to one tool, and have the tutorial explain things.
>
> Best
> Mike
>
>
>> On Mar 4, 2025, at 07:18, Josh Vermaas <vermaasj_at_msu.edu> wrote:
>>
>> Hi Charles,
>>
>> If you are building a psf/pdb from psfgen, the order of the atoms will be based on the order for the residue in the topology file (usually .top or .rtf). Here is the relevant section from top_all36_cgenff.rtf:
>>
>> RESI ETOH 0.00 ! C2H6O, Ethanol, adm jr.
>> GROUP
>> ATOM C1 CG321 0.05 ! H21 H11 H12
>> ATOM O1 OG311 -0.65 ! \ \ /
>> ATOM HO1 HGP1 0.42 ! H22--C2--C1
>> ATOM H11 HGA2 0.09 ! / \
>> ATOM H12 HGA2 0.09 ! H23 O1--HO1
>> GROUP
>> ATOM C2 CG331 -0.27
>> ATOM H21 HGA3 0.09
>> ATOM H22 HGA3 0.09
>> ATOM H23 HGA3 0.09
>>
>> You'll notice that your order matches here! The other thing that I notice is that you have a few atoms where the occupancy column is -1. That means that the input pdb for psfgen did not have an atom that matched the name that psfgen expected, and so nothing was loaded in. If you are doing this in a standard psfgen script, I think these two lines before you write out your psf/pdb will do the trick:
>>
>> regenerate angles dihedrals
>> guesscoord
>>
>>
>> -Josh
>>
>> On 3/3/25 9:34 PM, CHARLES MCCALLUM wrote:
>>> Hello, we recently starting learning to us Molefacture to parameterize, and we are running into some difficulties.
>>> Using the tutorial (https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf <https://urldefense.com/v3/__https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf__;!!HXCxUKc!05ug8JAR-3nPHBSss6MjnihamaigCYNB2fkqMBS_p9TkaoRVanfXqPDOuSym8SGF7WCqcAUQt445pzE$>) for ethanol, we are finding some coordinates are not being written out in the PDB file. We have edited the table as the tutorial notes.
>>>
>>> The console reports PSFGEN output, and all seems ok until it reports “failed to set coordinates” for H13, O2 and HO2 (for some reason I am not able to copy and paste the tkConsole output). The funny thing is, the output PDB contains more missing coordinates, and it has some labels wrong or missing, and it seems to have changed the order (shouldn’t these be in the order of the index in the table?):
>>>
>>> REMARK original generated coordinate pdb file
>>> ATOM 1 C1 ETOHL 1 0.000 0.000 0.000 1.00 0.00 L C
>>> ATOM 2 O1 ETOHL 1 0.000 0.000 0.000 -1.00 0.00 L
>>> ATOM 3 HO1 ETOHL 1 0.000 0.000 0.000 -1.00 0.00 L
>>> ATOM 4 H11 ETOHL 1 -0.326 0.946 -0.000 1.00 0.00 L H
>>> ATOM 5 H12 ETOHL 1 -0.326 -0.473 0.819 1.00 0.00 L H
>>> ATOM 6 C2 ETOHL 1 1.500 0.000 0.000 1.00 0.00 L C
>>> ATOM 7 H21 ETOHL 1 1.872 -0.103 1.042 1.00 0.00 L H
>>> ATOM 8 H22 ETOHL 1 1.899 -0.852 -0.592 1.00 0.00 L H
>>> ATOM 9 H23 ETOHL 1 0.000 0.000 0.000 -1.00 0.00 L
>>> END
>>>
>>> Writing out an xyz file does not cause problems:
>>> 9
>>> generated by VMD
>>> C 0.000000 0.000000 0.000000
>>> H -0.325568 0.945519 -0.000000
>>> H -0.325568 -0.472759 0.818843
>>> H -0.325568 -0.472759 -0.818843
>>> C 1.500000 0.000000 0.000000
>>> H 1.872000 -0.103000 1.042000
>>> H 1.899000 -0.852000 -0.592000
>>> O 2.059218 1.292080 -0.572891
>>> H 1.186122 2.396645 -0.844260
>>>
>>> We are also seeing occasional problems with the table deleting our edits, leaving blanks. When this happens, we have found we have to restart VMD in order to use Molefacture again.
>>>
>>> VMD 1.9.a57-x86_64-Rev12 on OS X 15.3.1
>>>
>>> Any help would be appreciated!
>>>
>>> Mike
>>>
>>> --
>>> Mike McCallum
>>> Morada/Stockton CA, USA
>>> cmccallum at me ^dot^ com
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>> --
>> Josh Vermaas
>>
>> vermaasj_at_msu.edu <mailto:vermaasj_at_msu.edu>
>> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
>> Michigan State University
>> vermaaslab.github.io
>
> --
> Mike McCallum
> Morada/Stockton CA, USA
> cmccallum at me ^dot^ com
>
>
>
>
>
>
> 

--
Mike McCallum
Morada/Stockton CA, USA
cmccallum at me ^dot^ com