I am trying to create AMBER prmtop and inpcrd files from CHARMM
param19_eef1 and toph19_eef1 parameter and topology files. I am using
CHAMBER, with the following command:
chamber -cmap \
-top toph19_eef1.inp \
-param param19_eef1.inp \
-psf input.psf \
-crd input.pdb \
-p output.prmtop \
-inpcrd output.inpcrd \
I get the following error however:
chemicalSymbolToZ() cannot map symbol: ! , to a Z value
NOTE: If the symbol reported above does not appear to be a valid
element then this most likely means your topology file does not
include element information. The code expects MASS lines in
the topology file to have the following format:
MASS 4 HT 1.00800 H ! TIP3P water hydrogen
your file most likely has
MASS 4 HT 1.00800
you should check this before proceeding.
chemicalSymbolToZ() failed to assign a Z value to an element
It seems the format of the topology file is not compatible. Is it possible
to create AMBER parameter and coordinate files with CHARMM implicit solvent
force fields?
Thanks,
Anna
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Received on Mon Jul 30 2012 - 15:00:02 PDT
