Respected,
I have nad+ frcmod, prepi and mol2 file, but in tleap when I'm adding in
complex files, I am facing this issue.
How should I resolve this error?
Kindly help me.
Error: For atom (.R<***** 1719>.A<C9 15>) could not find vdW (or other)
parameters for type (C.ar <
http://c.ar/>)
Error: For atom (.R<***** 1719>.A<O17 17>) could not find vdW (or other)
parameters for type (O.3)
*Script I am using:*
source /home/neuron3/bin/amber22/dat/leap/cmd/oldff/leaprc.ff99SB
source leaprc.water.tip3p
loadamberparams
/storage/priya/bin/amber22/dat/leap/parm/frcmod.ionsjc_tip3p
loadamberparams /home/neuron3/bin/amber22/dat/leap/parm/gaff.dat
protein = loadpdb recep_A_amber.pdb
saveamberparm protein receptor.prmtop receptor.inpcrd
loadamberprep nad.prepi
loadamberparams nad.frcmod
nad_lig = loadmol2 nad.mol2
loadamberprep tclh.prepi
loadamberparams tclh.frcmod
tclh_lig = loadmol2 tclh_out_ligand_01.mol2
complex = combine {protein nad_lig tclh_lig}
solvatebox complex TIP3PBOX 10.0
addions complex Na+ 0
addions complex Cl- 0
saveamberparm complex complex.prmtop complex.inpcrd
savepdb complex complex.pdb
quit
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- application/octet-stream attachment: nad.mol2
- application/octet-stream attachment: nad.prepi
Received on Sun Sep 21 2025 - 14:30:02 PDT
