[AMBER] TIP3p lennard jones parameters

From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Date: Fri, 25 Aug 2017 15:19:10 +0000

Dear all,

I have created my prmtop file in tleap and checked the validity in parmed.py
Unfortunately it gives the warning: Modified off-diagonal Lennard Jones parameters detected
I noticed that the TIP3P parameters in this file do not correspond to the literature (radius 3.15061; well depth 0.6364)
My values are 1.7683 and 0.1520 respectively.

Could this be triggering this warning? If not, how can I increase the verbosity in parmed.py to come to the bottom of this? Also, why does it differ from literature?

My tleap.in file is given below

source leaprc.ff14SB
source leaprc.gaff
addAtomTypes {
        { "X1" "N" "sp3" }
        { "X2" "N" "sp3" }
        { "X3" "O" "sp3" }
        { "Z1" "Zn" "sp3" }
        { "X4" "O" "sp3" }
#loadoff atomic_ions.lib
loadamberparams frcmod.ions1lsm_hfe_tip3p
HD1 = loadmol2 HD1.mol2
HD2 = loadmol2 HD2.mol2
GU1 = loadmol2 GU1.mol2
ZN1 = loadmol2 ZN1.mol2
WT1 = loadmol2 WT1.mol2
loadamberparams NDOM.frcmod
mol = loadpdb NDOM_mcpbpy.pdb
bond mol.361.NE2 mol.613.ZN
bond mol.365.NE2 mol.613.ZN
bond mol.389.OE1 mol.613.ZN
bond mol.613.ZN mol.614.O
bond mol.360.C mol.361.N
bond mol.361.C mol.362.N
bond mol.364.C mol.365.N
bond mol.365.C mol.366.N
bond mol.388.C mol.389.N
bond mol.389.C mol.390.N
savepdb mol NDOM_dry.pdb
saveamberparm mol NDOM_dry.prmtop NDOM_dry.inpcrd
solvatebox mol TIP3PBOX 10.0
addions mol Na+ 0
savepdb mol NDOM_solv.pdb
saveamberparm mol NDOM_solv.prmtop NDOM_solv.inpcrd

Kind regards

Lizelle Lubbe

PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
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Received on Fri Aug 25 2017 - 08:30:02 PDT
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