VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 30 2012 - 16:25:35 CDT

Hi Tristan,
  There's an ongoing issue with the combination of the new
CGENFF atom parameters and the standard versions of the PSF file format.
You didn't say which version of VMD you're using, but you would need to
use the latest test versions of VMD to get around this problem. The
root cause is that the standard versions of the PSF file format have
Fortran-based fix-field-width formats, that do not allow arbitrary-length
data. NAMD has been able to ignore the standard PSF formatting rules and
just accept anything that's a space delimited file, since it only reads
PSF files that come from a handful of sources all of which can generate
such files. VMD on the other hand, has to be rigorous and correctly parse
all of the non-NAMD file formats, and so if your PSF file doesn't have a
special "NAMD" tag in its header, the VMD PSF plugin will restrict the parsing
to the legal field widths, which will end up truncating your atom data.
If you use the latest test versions of VMD/NAMD/psfgen, this problem should
be solved already by generating PSF files that have this special "NAMD" tag
in them (the NAMD tag denotes the use of the space-delimited free-format
field widths that NAMD accepts, but that are incompatible with the standard
PSF file format specs).

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Jul 29, 2012 at 10:53:08AM +1000, Tristan Croll wrote:
> 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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-- 
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