Hi there,
I've been trying to set up the initial simulation conditions for some MD work using tleap and the following parameters:
source leaprc.protein.ff14SB #Source leaprc file for ff14SB protein force field
source leaprc.gaff #Source leaprc file for gaff
source leaprc.water.tip3p #source TIP3P water
loadamberparams frcmod.ionsjc_tip3p #source TIP3P ions
loadamberparams frcmod.ions234lm_126_tip3p #source TIP3P ions
mol = loadpdb PA0254_Apo_Dimer_Open_Clean_U.pdb #Load PDB file for protein
solvatebox mol TIP3PBOX 30 iso #Solvate the complex with a cubic water box 30 angstroms from complex
addions mol Cl- 0 #add Cl ions to neutralize the system
addions mol Na+ 0 #Add Na ions to neutralize the system
setBox mol vdw #Create Periodic Box
saveamberparm mol PA0254_ADOU_30.prmtop PA0254_ADOU_30.inpcrd #Save AMBER topology and coordinate files
savepdb mol PA0254_ADOU_30.pdb #Save resulting solvated box as pdb
quit #Quit tleap programme
tleap runs and outputs files, but when I check the output PDB I find that water and ion molecules are only present in about 60% of the box, with the central protein complex positioned at one face of it, and a few long oblong areas of water molecules protruding perpendicular from the face of the correctly generated solvent. I'm not seeing anything in the tleap log files that suggest an error with solvatebox, and when I've run this with a smaller box size (13 angstroms rather than 30) I get no problems. I'm using amber version 18 with ambertools 19.
Thanks and all the best,
Gabe
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Received on Fri Apr 16 2021 - 01:30:02 PDT
