Dear Experts,
I am trying to use spc/fw water.
My tleap file is like below.
source leaprc.protein.ff14SB
source leaprc.water.spce
addAtomTypes { { "ZN" "Zn" "sp3" } { "N5" "N" "sp3" } { "N6" "N" "sp3" } {
"N7" "N" "sp3" } { "O1" "O" "sp3" } }
#loadamberparams frcmod.ions1lm_126_tip3p
#HOH = SPG
loadAmberParams frcmod.spcfw
loadamberprep ZAFF.prep
loadamberparams ZAFF.frcmod
mol = loadpdb 2ili_protein+ZN6+waters.pdb
bond mol.259.ZN mol.92.NE2
bond mol.259.ZN mol.94.NE2
bond mol.259.ZN mol.117.ND1
bond mol.259.ZN mol.260.O
savepdb mol 2ili_dry.pdb
saveamberparm mol 2ili_dry.prmtop 2ili_dry.inpcrd
solvatebox mol SPCFWBOX 15.0
savepdb mol 2ili_spcfw.pdb
#addions mol Cl- Na+
#savepdb mol 2ili_solv.pdb
#saveamberparm mol 2ili_solv.prmtop 2ili_solv.inpcrd
But during the minimization run I got the following error.
Error: A residue defined as a "fast 3-point water"
is not defined by a triangle of three bonds.
Residue 315 contains 2 bonds.
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Wed Jun 04 2025 - 08:30:02 PDT
