Dear Bill, also Dear All,
I'm trying to make ionic liquid solvent box. But I'm still having hard
time. After running saveamberparm, I ran top2mol2 to check my structure. But
my ion structures have been changed. Some double bonds are changed to single
bonds
Attached herewith are original cation and anion structure files(emim.mol2
and tfo.mol2) I made, and result file(result.mol2) which has problem.
Before using structure files that I used, I made frcmod files and modify the
charge by using antechamber
I also attach Xleap log.
----------------------------------------------------------
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.gaff
----- Source: /usr/local/apps/amber9/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/apps/amber9/dat/leap/cmd/leaprc.gaff done Log
file: ./leap.log Loading parameters:
/usr/local/apps/amber9/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June,
2003)
> loadamberparams emim.frcmod
Loading parameters: ./emim.frcmod
Reading force field modification type file (frcmod) Reading title:
remark goes here
> loadamberparams tfo.frcmod
Loading parameters: ./tfo.frcmod
Reading force field modification type file (frcmod) Reading title:
remark goes here
> list
gaff
> emim=loadmol2 emim.mol2
Loading Mol2 file: ./emim.mol2
Reading MOLECULE named MOL
> tfo=loadmol2 tfo.mol2
Loading Mol2 file: ./tfo.mol2
Reading MOLECULE named MOL
> x=copy emim
> solvatebox x tfo 4
Solvent has no box, so preparing by making box including vdw (Use 'setBox
centers' first if box was pre-equilibrated)
Solute vdw bounding box: 10.325 6.861 5.901
Total bounding box for atom centers: 18.325 14.861 13.901
Solvent unit box: 7.072 6.078 6.900
Total vdw box size: 21.215 12.515 6.900 angstroms.
Volume: 1831.891 A^3
Total mass 409.308 amu, Density 0.371 g/cc
Added 2 residues.
> solvatebox x emim 3.5
Solvent has no box, so preparing by making box including vdw (Use 'setBox
centers' first if box was pre-equilibrated)
Solute vdw bounding box: 21.215 12.515 6.900
Total bounding box for atom centers: 28.215 19.515 13.900
Solvent unit box: 10.325 6.861 5.901
Total vdw box size: 30.564 20.878 6.900 angstroms.
Volume: 4402.831 A^3
Total mass 520.476 amu, Density 0.196 g/cc
Added 1 residues.
> edit x
> check x
Checking 'x'....
Checking parameters for unit 'x'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> saveamberparm x iobox.prmtop iobox.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 10 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
NIT1 2
NIT2 2
)
(no restraints)
>
-----------------------------------------------------------------
I'm very beginning of amber. Please reply in detail. Thank for your kind
help in advance.
Regards,
Hoshin Kim
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of Bill Ross
Sent: Tuesday, May 04, 2010 5:06 AM
To: amber.ambermd.org
Subject: Re: [AMBER] How to make ionic liquid solvent box?
> I am trying to do dynamics regarding solvation sugar molecules in
> ionic liquids. Could anyone help me how to create the ionic liquid
> solvent box using xleap? Ionic liquid that I will try to use is
> [Emim][TfO] (1-ethyl-3-methylimidazolium Trifluoromethylsulfonate).
>
> Ionic liquid is the liquid that is only composed of anion and cation.
> In case of [Emim][TfO], Emim(1-ethyl-3-methylimidazolium) is
> cation(+1),
> [TfO](Trifluoromethylsulfonate) is anion(-1).
You could make an initial box by solvating a single molecule in
layers:
> init = copy mol1
> solvatebox init mol2 4
> solvatebox init mol1 2
> saveamberparm init iobox.top iobox.crd
Then equilibrate the box with constant pressure, convert to pdb, and
> solbox = loadpdb solbox.pdb
> solvatebox mymol solbox 10
Or you could build up the layers directly around your solute, then put a
cartestian restraint on the solute while equilibrating it (as would also be
necessary if using an intermediate box to solvate the solute).
Likely it will be tricky to get 1:1 ionic ratio, but this will not matter so
much if you are making an ion-only box to then solvate another molecule,
since arbitrary adjustments will still be needed after solvating the other
molecule because of losing the ionic balance. The adjustments can be made by
editing the system in xleap and deleting extra solute molecules of the
appropriate species.
You might want to consider debugging your solvent molecules by first running
each separately with Na+ and Cl- to neutralize.
Bill
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- application/octet-stream attachment: tfo.mol2
- application/octet-stream attachment: emim.mol2
Received on Tue May 04 2010 - 16:00:03 PDT
