VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Jun 04 2012 - 09:41:59 CDT

Francesco,

As I have told you previously in direct correspondence, the problem is due to improper atom names as shown in the debugging file here:

>QM TARGET DATA SECTION
>baseLog: /home/francesco/work_3LEZ_charmm27FF/mod2-CLV_FFTK_CHARMM/single-point_energy.log
>watLog: /home/francesco/work_3LEZ_charmm27FF/mod2-CLV_FFTK_CHARMM/single-point_energy_water.log
>logFileList:
> /home/francesco/....../CLV-ACC-O1.gau.log
> /home/francesco/...../CLV-ACC-O1-m120.gau.log
> /home/francesco/...../CLV-ACC-O1-p120.gau.log
> /home/francesco/..../CLV-ACC-O4.gau.log
> /home/francesco/...../CLV-ACC-O4-m120.gau.log
> /home/francesco/........./CLV-ACC-O4-p120.gau.log
> /home/francesco/......../CLV-ACC-O5.gau.log
> /home/francesco/......../CLV-ACC-O5-m120.gau.log
> /home/francesco/.........../CLV-ACC-O5-p120.gau.log
> /home/francesco/........./CLV-DON-H8.gau.log
>atomList: O1.gau O1-m120.gau O1-p120.gau O4.gau O4-m120.gau
>O4-p120.gau O5.gau O5-m120.gau O5-p120.gau H8.gau
>indWeights: 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0

Upon loading the log files into the QM target data section, ffTK tries to automatically fill out the "atom name" column by parsing the relevant information from the filename. It expects log filenames to follow the form: <resname>-<DON or ACC>-<atom name>.log. The .gau.log m120/p120 extensions included in your filenames fully compliant with what the parser expects. This yields incorrect settings for the atom names, as evidenced from the atom list and the resulting error message thrown by ffTK. You need to manually edit the "Atom Name" properly in the qm target data section to give the proper atom names (e.g., O1 rather than O1.gau).

Chris