AMBER Archive (2009)

Subject: RE: [AMBER] database

From: Jeff Yeo (
Date: Thu Sep 17 2009 - 16:01:48 CDT

Here is the way I do it:1) Use a molecular modeling package to create the following files:i) Protein-Ligand-complex.pdb file (protein not protonated, ligand is protonated)ii) myligand.pdb file (simply delete the protein from the step above)
2) Use the command:$AMBERHOME/exe/antechamber -i myligand.pdb -fi pdb -o -fo gcrt
3) Start Gaussian 03. File –> Open –> myligand.comClick the “Run” button. Wait patiently.
4) Convergence is achieved, i.e. wait is finally over.
5) Gaussian output is in myligand.out.
6) Next, run:$AMBERHOME/exe/antechamber -i myligand.out -fi gout -o myligand.prepi -fo prepi -c resp -s 2
7) Test if all the parameters that you require are available.$AMBERHOME/exe/parmchk -i myligand.prepi -f prepi -o myligand.frcmod
8) Run tLeap:$AMBERHOME/exe/tleapsource leaprc.gaffloadamberprep myligand.prepilistloadamberparams myligand.frcmodcheck MOLsavepdb MOL myligand.pdbquit
9) Remove all atoms belong to the ligand Protein-Ligand-complex.pdb file by manually editing it. Also remove "END". Save changes.
10) Next, I concatenate: cat Protein-Ligand-complex.pdb myligand.pdb> complex.pdb
11) Run tleap:$AMBERHOME/exe/tleapsource leaprc.gaffloadAmberPrep myligand.prepilistloadamberparams myligand.frcmodcheck MOLsource leaprc.ff99SBcomplex = loadpdb complex.pdbcheck complexaddions complex Na+ 0addions complex Cl- 0check complexsaveAmberParm complex complex.crdsolvateoct complex TIP3PBOX 10.0saveAmberParm complex complex_solvated.crdquit

Hope it helps. =)
Jeff YeoGrad StudentNational University of Singapore
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