Dear amber users,
I have been preparing files for MD with following protocol and then later calculating MM/GBSA. I have been doing that with lot of files BUT recently I encountered error in two files while calculating binding free energy. Can you tell me what is wrong
# Ligand preparation using antechamber
antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s 2 -nc {charge of the ligand}
parmchk -i ligand.mol2 -f mol2 -o ligand.frcmod
#leaprc
source leaprc.ff12SB
source leaprc.gaff
loadamberparams frcmod.ionsjc_tip3p
UNK = loadmol2 ligand.mol2
loadamberparams ligand.frcmod
saveoff UNK ligand.lib
saveamberparm UNK ligand.prmtop ligand.inpcrd
receptor = loadpdb protein.pdb
saveamberparm receptor receptor.prmtop receptor.inpcrd
savepdb receptor receptor.pdb
saveoff receptor receptor.lib
comp = combine {receptor UNK}
saveamberparm comp complex.prmtop complex.inpcrd
savepdb comp complex.pdb
saveoff comp complex.lib
addions comp Na+/Cl- 0
solvateoct comp TIP3PBOX 12.0
saveamberparm comp complex_solvated.prmtop complex_solvated.inpcrd
savepdb comp complex_solvated.pdb
saveoff comp complex_solvated.lib
quit
#MM/GBSA
Input file for running PB and GB
&general
startframe=1500, verbose=1,entropy=1,
/
&gb
igb=2, qm_theory = 'PM3', saltcon=0.100
/
&decomp
idecomp=2, dec_verbose= 2
/
#error
CalcError: sander failed with prmtop complex.prmtop!
Regards,
Nitin Sharma
Department of Pharmacy,Faculty of Science,National University of Singapore,block S7, Level 2, 18 science drive 4, Singapore 117543, Republic of Singapore: sharmanitin.nus.edu.sg<mailto:sharmanitin.nus.edu.sg> ; Phone +6582969643; http://www.linkedin.com/in/imsharmanitin
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Received on Thu Apr 24 2014 - 07:30:03 PDT
