Revision as of 14:15, 19 March 2018

2nnq with an explicit solvent model

Prepare the files

Convert 2nnq.lig.withH.charged.mol2 to pdb in chimera

Convert 2nnq.rec.withH.charged.mol2 to pdb in chimera

Copy into zzz.master

Move into 000.programs

Paramaterize the ligand

antechamber -i ../zzz.master/2nnq.lig.withH.charged.pdb -fi pdb -o 2nnq_lig.am1bcc.mol2 -fo mol2 -at gaff2 -c bcc -rn LIG -nc 1

Check for missing force field parameters

parmchk2 -i 2nnq_lig.am1bcc.mol2 -f mol2 -o 2nnq_lig.am1bcc.frcmod

Move into 001.tleap_build

Create tleap.build.in file

Create Amber topology and coordinates files for the MD simulation

tleap -f tleap.build.in

@@ Line 23: / Line 23: @@
 Move into 001.tleap_build
+Create tleap.build.in file
+Create Amber topology and coordinates files for the MD simulation
+ tleap -f tleap.build.in