Dear AMBER,
I tried to use parmed to convert a gromacs file that has 3 MG ions in it to
AMBER format using the commands:
gromber nacl.top nacl.gro
outparm nacl.AMBER.top
writeCoordinates nacl.AMBER.crd
quit()
However if I then run
ambpdb -p nacl.AMBER.top < nacl.AMBER.crd > nacl.AMBER.pdb
to get a pdb and look at the pdb the MG ions are missing. Does anyone have
any idea of what is going on? It looks like there are MG ions listed in the
nacl.AMBER.top topology file.
Thanks,
Holly Freedman
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Received on Thu Jun 07 2018 - 17:00:02 PDT
