Dear amber experts,
I found at the website (www.pharmacy.man.edu.ac.uk/amber) frcmod and prepin
files for ca2+ ion.
In tleap, I load these two files and then read in the pdb file. Tleap does
not complain. However,
when I ask what the charge is of the system, the '2+' from the calcium ion
is not recognised and I am
told that the charge of the system is that without the ion. Consequently,
when I use addions2 to
neutralize the system, tleap adds 6 positive counter-ions rather than 4.
Is this normal or have I done something wrong?
I have also found in parm99.dat another reference to Ca2+ . The calcium ion
called 'C0',
however I do not know what the unit name should be. For comparison, the atom
name for the Ca2+ ion
from the manchester university site is KA and the unit is CAL. So, if I am
using the atom name C0, what
is the unit name (the ??? in the extract from the pdb file below).
TER
HETATM 1398 C0 ??? A 90 -2.611 15.599 11.115
TER
many thanks in advance for any advice,
JC.
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Received on Sun Sep 16 2007 - 06:07:36 PDT
