Hi,
I am trying to run an mmpbsa calculation using the perl script. I have
created the input topology files for complex, ligand and receptor. However
upon submission the job does not complete properly. The error I have been
able to find is in the file X_ThX_Complex_com.pdb.1:
ERROR: Flag "RADII" not found in PARM file
If I load my parm files into ptraj i also get the following errors related
to the generalised born intrinsic dielectric radii:
PRMTOP does not contain %FLAG RADIUS_SET
PRMTOP does not contain %FLAG RADII
PRMTOP does not contain %FLAG SCREEN
The following is an example set-up file I use to create the parm files. Is
there a command I am missing that sets the radii?
##########
source leaprc.gaff
source leaprc.ff03.r1
loadoff all_aminoct02.lib
loadoff ${dirNo}_final.lib
mol = loadpdb ${dirNo}_complex_unsolvated.pdb
bond mol.64.SG mol.157.SG
solvatebox mol TIP3PBOX 10.0
charge mol
#addions2 mol K+ 14.0
#savepdb mol ${dirNo}_complex_SOLVATED.pdb
saveamberparm mol dehydrated2a_${dirNo}.parm dehydrated2a_${dirNo}.crd
(i later use rdparm to strip out the water molecules to create the
dehydrated complex)
#######
Any help would be greatly appreciated.
Best regards,
ET
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Received on Wed Feb 29 2012 - 05:00:01 PST
