Hi,
I am trying to incorporate Mn parameters using the following steps:
bsub -P Pan -app amber-mpich -Is -q interactive tleap -f leaprc.ff99SB
source leaprc.gaff
mods = loadAmberParams "frcmod.Mn" which I downloaded from
http://www.pharmacy.manchester.ac.uk/bryce/amber#ion
Mn= loadpdb Mn.pdb (I saved the coordinates of Mn and protein separately in this file)
check Mn
FATAL: Atom .R<MN 303>.A<MN 1> does not have a type.
FATAL: Atom .R<MN 304>.A<MN 1> does not have a type.
The pdb file has only protein and MN atoms. Mn atom coordinates are as follows:
HETATM 1520 MG+ MG+ D 303 -14.664 -20.531 -22.254 1.00 59.85 MG2
Appreciate any help/suggestion in this regard.
Thanks and regards,
Latha.
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Received on Fri Jun 07 2013 - 12:30:03 PDT
