RE: [AMBER] How to make ionic liquid solvent box? from Hoshin Kim on 2010-05-04 (Amber Archive May 2010)

From: Hoshin Kim <heisen85.hanmail.net>
Date: Wed, 05 May 2010 06:06:39 +0900 (KST)

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 Dear Bill,
 
 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. 
Attached herewith are original cation and anion structure files(.mol2) I 
made, and result file 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: <a href="mailto:amber-bounces.ambermd.org" style="color: rgb(0, 84, 136); ">amber-bounces.ambermd.org</a> [mailto:<a href="mailto:amber-bounces.ambermd.org" style="color: rgb(0, 84, 136); ">amber-bounces.ambermd.org</a>] On Behalf 
Of Bill Ross 
Sent: Tuesday, May 04, 2010 5:06 AM 
To: <a href="mailto:amber.ambermd.org" style="color: rgb(0, 84, 136); ">amber.ambermd.org</a> 
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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This is MIME Epilogue

application/octet-stream attachment: emim.mol2

application/octet-stream attachment: tfo.mol2

application/octet-stream attachment: result.mol2

Received on Tue May 04 2010 - 14:30:03 PDT