VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Fri Mar 07 2025 - 09:50:39 CST

Hi Paweł, thank you for reporting this bug in Molefacture.
I'm glad you found a workaround :)

I'll add it to our list of Bugs on GitLab to resolve it ASAP.

Friendly,
Diego.

On Wed, Mar 5, 2025 at 2:58 AM Paweł Kędzierski <pawel.kedzierski_at_pwr.edu.pl>
wrote:

> Dear All,
>
> There is a related bug in Molefacture 2 affecting FFTK users. When you do
> not make any changes but just want to save the topology file, it is not
> saved without any message.
>
> The Josh suggestion cited below may therefore not work in general.
> Actually what I observe that in these workflows when saving PSF+PDB files
> for a new ligand does actually work, Molefacture ALSO saves the top file
> with the same prefix. So perhaps the primary cause of both bugs is that
> sometimes Molefacture "forgets" to create the the TOP file which is needed
> by psfgen to create the PDB+PSF pair.
>
> Now the problem I observe:
> When using FFTK, one ends up with PDB and PSF files. I use Molefacture to
> covert the PSF to a TOP file format to be used with the regular system
> preparation procedure.
> The steps to reproduce:
> - load a molecule from PSF and PDB files,
> - open Molefacture
> - Molefacture menu File-> New molecule -> From selection, type "all"
> - Molefacture menu File-> Write top/str file
> Neither str nor top format works, nothing is written. Saving xyz or mol2
> formats does work.
> When I tried to save psf+pdb pair of files, vmd actually crashed (tested
> with the distributed binary version 1.9.4a57 for Linux) with these messages:
>
> psfgen) building segment O1
> psfgen) reading residues from pdb file O1.pdb
> psfgen) unknown residue type MSA
> psfgen) extracted 1 residues from pdb file
> psfgen) setting patch for first residue to NONE
> psfgen) setting patch for last residue to NONE
> psfgen) enabling angle autogeneration
> psfgen) enabling dihedral autogeneration
> Info: generating structure...
> psfgen) unknown residue type MSA
> double free or corruption (out)
>
> I have found a workaround, namely if you introduce any change in the
> Molefacture editor, even something like oxidation state of any atom
> (irrelevant for the TOP file), then you can save the TOP file and the
> PSF+PDB files normally. But it is clearly a bug.
>
> As for the topic cited, I think I remember that the issue with all-zero
> PDB coords only happend to me when the molecule was read from a PDB file.
> When I start with the ligand read from a MOL2 file, the problem does not
> appear, but again I have to do some editing first to be able to save the
> PSF+PDB files for FFTK.
>
> Best regards,
> Paweł
>
> W dniu 4.03.2025 o 19:11, Josh Vermaas pisze:
>
> Hi Mike,
>
> Yeah, there have been changes to molefacture since 2015, and I think that
> none of the currently listed maintainers are still actively working on VMD,
> so it wouldn't surprise me that there is a bug *somewhere*. I can reproduce
> that a psf/pdb written from molefacture based on the tutorial gives you
> zeros for all the coordinates, but the xyz files work!
>
> Now, I can sort of see where this goes wrong. Its in the
> molefacture/molefacture_internals.tcl file, in the write_psfpdbfiles
> procedure, lines 2756-2800 is what is actually being used to build the
> psf/pdb. Note that by default, VMD's new and improved molefacture tries to
> be clever, and will load topology files that already are distributed with
> VMD, including top_all36_cgenff.rtf (which has a ETOH residue defined in
> it). To do what you want it to, you'll need to create another topology file
> for the molecule you made in molefacture first (File->write top/str file),
> which is appended to the list of topology files in your psfcontext. Only
> after you write this top/str file, will psfgen recognize the atoms and put
> them in the right place.
>
> Hope this helps!
>
> -Josh
>
> On 3/4/25 12:23 PM, CHARLES MCCALLUM wrote:
>
> 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>
> <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>
> <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
> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
> Michigan State Universityvermaaslab.github.io
>
>
> --
> Mike McCallum
> Morada/Stockton CA, USA
> cmccallum at me ^dot^ com
>
>
>
>
>
>
>
>
> --
> Mike McCallum
> Morada/Stockton CA, USA
> cmccallum at me ^dot^ com
>
>
>
>
>
>
>
>
> --
> Josh Vermaas
> vermaasj_at_msu.edu
> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
> Michigan State Universityvermaaslab.github.io
>
>
>
> --
> Room 3.03 A-3, tel. +48 71 320 3200
> email: Pawel.Kedzierski_at_pwr.edu.pl
> Institute of Advanced Materials I01W03D10
> Faculty of Chemistry
> Wrocław University of Science and Technology
> Wrocław, Poland
>
> 

-- 
Diego Enry B. Gomes, PhD
Department of Physics at Auburn University &
NIH Center for Macromolecular Modeling and Visualization
Leach Science Center - Ste. 3182 - Auburn, AL
dgomes_at_auburn.edu