VMD-L Mailing List

From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Tue Mar 04 2025 - 09:18:20 CST

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 University
vermaaslab.github.io