Hi Patrick,
As far as I am aware the Z value is only needed for the assignment of GB
Radii since the Charmm psf file does not provide these. I don't think there
are GB radii in the code for Iron so as long as you are only planning on
running explicit solvent PME simulations with the resulting prmtop you
should be safe doing what you propose.
All the best
Ross
> -----Original Message-----
> From: Patrick von Glehn [mailto:patrickvonglehn.gmail.com]
> Sent: Wednesday, August 17, 2011 9:21 AM
> To: amber.ambermd.org
> Subject: [AMBER] Iron in CHAMBER: chemicalSymbolToZ() cannot map
> symbol: FE, to a Z value
>
> Hi all,
>
> I'm converting my iron containing system from charmm type input files
> to amber type using CHAMBER and I came across the following error:
>
> chemicalSymbolToZ() cannot map symbol: FE, to a Z value
>
> I found the cause of the problem. In the source code (file
> $AMBERHOME/AmberTools/src/chamber/psfprm.f) there is a list of
> chemical symbols and corresponding Z values which doesn't contain an
> entry for FE.
>
> I don't know the purpose of mapping chemical symbols to Z values. Is
> an acceptable solution to simply add an entry for FE in the source
> code and then recompile AmberTools?
>
> Thanks in advance for you help,
>
> Patrick
>
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Received on Wed Aug 17 2011 - 10:00:03 PDT
