From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Sat Jul 28 2012 - 19:53:08 CDT

Hi,

I've been running a few simulations involving a small molecule (sphingosylphosphorylcholine, SPC) parameterised using the ParamChem server. The simulations I've just started running have the amine group on SPC deprotonated. When visualising this, I got something of a shock when I asked VMD to colour the atoms by charge - it was reporting the charge on each of the two amine hydrogens as +2.0.

Reassuringly, the charges in the stream file are fine:

ATOM N51 NG321 -0.987 ! 22.978
ATOM H511 HGPAM2 0.341 ! 1.518
ATOM H512 HGPAM2 0.341 ! 1.518

... as are those in the AutoPSF-generated PSF file:

    9197 O2 153 SPUD N51 NG321 -0.987000 14.0070 0
    9198 O2 153 SPUD H511 HGPAM2 0.341000 1.0080 0
    9199 O2 153 SPUD H512 HGPAM2 0.341000 1.0080 0

The NAMD output also reports the total system charge correctly:

Info: TOTAL CHARGE = 6.65523e-06 e

VMD reports the atom types as "HGPA" - my guess is that the parser only allows four characters for the atom type, so when fed HGPAM2 has ignored the M and taken 2 as the charge.

Cheers,

Tristan

Tristan Croll
Lecturer
Faculty of Health
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443

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