Hi,
Maybe I'm missing something, but why are you using 'setbox' after
'solvatebox'? I recommend removing the 'setbox' command ('solvatebox'
creates an orthogonal unit cell for you), and using 'addionsrand'
instead of 'addions'; the former tends to be much faster and to be
honest I've never really come across an instance where 'addions' is
demonstrably better (maybe others on the list can correct me). In
addition, you're first neutralizing with Cl-, but then trying to
neutralize with Na+, so one of your 'addions' command is going to do
nothing I think. If you are going to add both cations and anions you
should have specific numbers of each in mind. Otherwise, just add ions
of the proper charge to neutralize your system. Also,
'leaprc.water.tip3p' already loads ions - you shouldn't need to load
the FRCMOD files yourself. So, try something like this:
source leaprc.protein.ff14SB
source leaprc.gaff
source leaprc.water.tip3p
mol = loadpdb PA0254_Apo_Dimer_Open_Clean_U.pdb
solvatebox mol TIP3PBOX 30 iso
addionsrand mol Cl- <# Cl-> Na+ <#Na+>
saveamberparm mol PA0254_ADOU_30.prmtop PA0254_ADOU_30.inpcrd
savepdb mol PA0254_ADOU_30.pdb
quit
Hope this helps,
-Dan
On Fri, Apr 16, 2021 at 4:02 AM Gabriel Titchiner
<gabriel.titchiner.manchester.ac.uk> wrote:
>
> 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 - 07:30:02 PDT
