VMD-L Mailing List

From: CHARLES MCCALLUM (cmccallum_at_me.com)
Date: Mon Mar 03 2025 - 20:34:12 CST

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) 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