Date: Mon, 29 Apr 2024 15:55:17 +0000
Hello to all !
I'm trying to solve a system that has a membrane and a protein inserted. I built the membrane in CHARMMGUI, and when I try to solvate the system in tleap, it places water molecules in the hydrophobic part of the system, I don't know how to make it only place them in the Z axis.
I am using these commands:
tleap -f oldff/leaprc.ff14SB
source leaprc.gaff
source leaprc.lipid14
loadamberparams frcmod.ionsjc_tip3p
loadamberparams ABC.frcmod #ABC =ligand that is inside of a protein
loadoff ABC.lib
com = loadpdb com_m.pdb #com_m.pdb complex with protein, ligand, internal ions, membrane, waters and external ions
solvatebox com TIP3PBOX {0,0,15}
addionsrand com Na+ 123 Cl- 124 (the sistem has charge +1)
bond com.111.SG com.222.SG
saveamberparm com .... #to save .prmtop and .inpcrd files
savepdb com ... #to save .pfb file
if it helps, i show you an example of the waters in the border of box
-Matías
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