Dear amber users,
Recently, I used MCPB to research my complex. everything looks ok, but when I used tleap to generate the top and crd file, there were some errors occur:
FATAL: Atom .R<TR1 231>.A<O1 22> does not have a type.
FATAL: Atom .R<TR1 231>.A<O2 23> does not have a type.
FATAL: Atom .R<TR1 231>.A<O3 24> does not have a type.
FATAL: Atom .R<TR1 231>.A<C4 25> does not have a type.
FATAL: Atom .R<TR1 231>.A<C5 26> does not have a type.
FATAL: Atom .R<TR1 231>.A<C6 27> does not have a type.
FATAL: Atom .R<TR1 231>.A<C7 28> does not have a type.
I know, these errors may caused by missing the parameters for the ligand TR1. But I have generated and loaded the frcmod file for it, my tleap.in file was as list:
source leaprc.ff14SB
source leaprc.gaff
addAtomTypes {
{ "X1" "N" "sp3" }
{ "X2" "N" "sp3" }
{ "X3" "N" "sp3" }
{ "X4" "O" "sp3" }
{ "Z1" "Zn" "sp3" }
{ "X5" "O" "sp3" }
}
loadoff atomic_ions.lib
loadamberparams frcmod.ions1lsm_hfe_tip3p
HD1 = loadmol2 HD1.mol2
HD2 = loadmol2 HD2.mol2
HD3 = loadmol2 HD3.mol2
TR1 = loadmol2 TR1.mol2
ZN1 = loadmol2 ZN1.mol2
WT1 = loadmol2 WT1.mol2
loadamberparams ligand.frcmod
loadamberparams mp.frcmod
mol = loadpdb mp_mcpbpy.pdb
bond mol.150.NE2 mol.229.ZN
bond mol.154.NE2 mol.229.ZN
bond mol.160.NE2 mol.229.ZN
bond mol.190.OH mol.229.ZN
bond mol.229.ZN mol.230.O
bond mol.149.C mol.150.N
bond mol.150.C mol.151.N
bond mol.153.C mol.154.N
bond mol.154.C mol.155.N
bond mol.159.C mol.160.N
bond mol.160.C mol.161.N
bond mol.189.C mol.190.N
bond mol.190.C mol.191.N
savepdb mol mp_dry.pdb
saveamberparm mol mp_dry.prmtop mp_dry.inpcrd
solvatebox mol TIP3PBOX 10.0
addions mol Na+ 0
addions mol Cl- 0
savepdb mol mp_solv.pdb
saveamberparm mol mp_solv.prmtop mp_solv.inpcrd
quit
Is there any special settings should be make?
I need your help!
Thanks and Best Regards!
Sincerely,
Xiaofeng
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Received on Thu Apr 21 2016 - 19:30:06 PDT
