Dear all,
I have faced an issue in tleap for preparation of. top and .rst files for my protein-ligand complex. There are 2 chlorine atoms in ligand structure, and I have used GAFF for the ligand atom. I have used .prep, .lib and .frcmod files for ligand but there is still problem:
FATAL: Atom .R<SDF 369>.A<CL72 72> does not have a type.
FATAL: Atom .R<SDF 369>.A<CL82 73> does not have a type.
Any help will be appreciated.
Bests
Zahra
I have used these commands for running antechamber and tleap:
in antechamber:
antechamber -i lig-WithH.pdb -fi pdb -nc 0 -o lig-WithH.mol2 -fo mol2 -c bcc -s 2
parmchk2 -i lig-WithH.mol2 -f mol2 -o lig-WithH.frcmod
in tleap:
source leaprc.ff99SB
source leaprc.gaff
source leaprc.water.tip3p
set default pbradii mbondi2
loadAmberParams frcmod.ionsjc_tip3p
loadmol2 lig-WithH.mol2
loadamberprep lig-WithH.prep
loadamberparams lig-WithH.frcmod
loadoff lig-WithH.lib
complex = loadpdb lig-complex.pdb
solvatebox complex TIP3PBOX 15.0 2.00
addions complex Na+ 8
saveamberparm complex lig-complex.top lig-complex.rst
savepdb complex lig-complex-tleap.pdb
quit
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Received on Tue Mar 16 2021 - 00:30:02 PDT
