RE: [AMBER] How to make ionic liquid solvent box?

From: Å·¾Æ±âµÅÁö <heisen85.hanmail.net>
Date: Wed, 05 May 2010 05:42:20 +0900 (KST)

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<span class="Apple-style-span" style="color: rgb(0, 0, 0); font-family: arial, sans-serif; line-height: normal; border-collapse: collapse; "><br>
&nbsp;I'm trying to make ionic liquid solvent box. But I'm still having hard<br>
time. After running saveamberparm, I ran top2mol2 to check my structure. But<br>
my ion structures have been changed.<br>
Attached herewith are original cation and anion structure files(.mol2) I<br>
made, and result file which has problem.<br>
Before using structure files that I used, I made frcmod files and modify the<br>
charge by using antechamber<br>
<br>I also attach Xleap log.<br>
------------------------------<wbr>----------------------------<br>
Welcome to LEaP!<br>
(no leaprc in search path)<br>
&gt; source leaprc.gaff<br>
----- Source: /usr/local/apps/amber9/dat/<wbr>leap/cmd/leaprc.gaff<br>
----- Source of /usr/local/apps/amber9/dat/<wbr>leap/cmd/leaprc.gaff done<br>
Log file: ./leap.log<br>
Loading parameters: /usr/local/apps/amber9/dat/<wbr>leap/parm/gaff.dat<br>
Reading title:<br>
AMBER General Force Field for organic mol., add. info. at the end (June,<br>
2003)<br>
&gt; loadamberparams emim.frcmod<br>
Loading parameters: ./emim.frcmod<br>
Reading force field modification type file (frcmod)<br>
Reading title:<br>
remark goes here<br>
&gt; loadamberparams tfo.frcmod<br>
Loading parameters: ./tfo.frcmod<br>
Reading force field modification type file (frcmod)<br>
Reading title:<br>
remark goes here<br>
&gt; list<br>
gaff<br>
&gt; emim=loadmol2 emim.mol2<br>
Loading Mol2 file: ./emim.mol2<br>
Reading MOLECULE named MOL<br>
&gt; tfo=loadmol2 tfo.mol2<br>
Loading Mol2 file: ./tfo.mol2<br>
Reading MOLECULE named MOL<br>
&gt; x=copy emim<br>
&gt; solvatebox x tfo 4<br>
Solvent has no box, so preparing by making box including vdw<br>
(Use 'setBox centers' first if box was pre-equilibrated)<br>
&nbsp;Solute vdw bounding box: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;10.325 6.861 5.901<br>
&nbsp;Total bounding box for atom centers: &nbsp;18.325 14.861 13.901<br>
&nbsp;Solvent unit box: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 7.072 6.078 6.900<br>
&nbsp;Total vdw box size: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 21.215 12.515 6.900 angstroms.<br>
&nbsp;Volume: 1831.891 A^3<br>
&nbsp;Total mass 409.308 amu, &nbsp;Density 0.371 g/cc<br>
&nbsp;Added 2 residues.<br>
&gt; solvatebox x emim 3.5<br>
Solvent has no box, so preparing by making box including vdw<br>
(Use 'setBox centers' first if box was pre-equilibrated)<br>
&nbsp;Solute vdw bounding box: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;21.215 12.515 6.900<br>
&nbsp;Total bounding box for atom centers: &nbsp;28.215 19.515 13.900<br>
&nbsp;Solvent unit box: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 10.325 6.861 5.901<br>
&nbsp;Total vdw box size: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 30.564 20.878 6.900 angstroms.<br>
&nbsp;Volume: 4402.831 A^3<br>
&nbsp;Total mass 520.476 amu, &nbsp;Density 0.196 g/cc<br>
&nbsp;Added 1 residues.<br>
&gt; edit x<br>
<br>&gt; check x<br>
Checking 'x'....<br>
Checking parameters for unit 'x'.<br>
Checking for bond parameters.<br>
Checking for angle parameters.<br>
Unit is OK.<br>
&gt; saveamberparm x iobox.prmtop iobox.inpcrd<br>
Checking Unit.<br>
Building topology.<br>
Building atom parameters.<br>
Building bond parameters.<br>
Building angle parameters.<br>
Building proper torsion parameters.<br>
Building improper torsion parameters.<br>
&nbsp;total 10 improper torsions applied<br>
Building H-Bond parameters.<br>
Not Marking per-residue atom chain types.<br>
Marking per-residue atom chain types.<br>
&nbsp;(Residues lacking connect0/connect1 -<br>
&nbsp; these don't have chain types marked:<br>
<br>&nbsp; &nbsp; &nbsp; &nbsp;res &nbsp; &nbsp; total affected<br>
<br>&nbsp; &nbsp; &nbsp; &nbsp;NIT1 &nbsp; &nbsp;2<br>
&nbsp; &nbsp; &nbsp; &nbsp;NIT2 &nbsp; &nbsp;2<br>
&nbsp;)<br>
&nbsp;(no restraints)<br>
&gt;<br>
------------------------------<wbr>------------------------------<wbr>-----<br>
I'm very beginning of amber. Please reply in detail. Thank for your kind<br>
help in advance.<br>
<br>Regards,<br>
<br>Hoshin Kim<br>
<br>-----Original Message-----<br>
From:&nbsp;<a href="mailto:amber-bounces.ambermd.org" style="color: rgb(0, 84, 136); ">amber-bounces.ambermd.org</a>&nbsp;[mailto:<a href="mailto:amber-bounces.ambermd.org" style="color: rgb(0, 84, 136); ">amber-bounces.ambermd.<wbr>org</a>] On Behalf<br>
Of Bill Ross<br>
Sent: Tuesday, May 04, 2010 5:06 AM<br>
To:&nbsp;<a href="mailto:amber.ambermd.org" style="color: rgb(0, 84, 136); ">amber.ambermd.org</a><br>
Subject: Re: [AMBER] How to make ionic liquid solvent box?<br>
<br>&gt; I am trying to do dynamics regarding solvation sugar molecules in<br>
&gt; ionic liquids. Could anyone help me how to create the ionic liquid<br>
&gt; solvent box using xleap? Ionic liquid that I will try to use is<br>
&gt; [Emim][TfO] (1-ethyl-3-methylimidazolium Trifluoromethylsulfonate).<br>
&gt;<br>
&gt; Ionic liquid is the liquid that is only composed of anion and cation.<br>
&gt; In case of [Emim][TfO], Emim(1-ethyl-3-<wbr>methylimidazolium) is<br>
&gt; cation(+1),<br>
&gt; [TfO](<wbr>Trifluoromethylsulfonate) is anion(-1).<br>
<br>You could make an initial box by solvating a single molecule in<br>
layers:<br>
<br>&gt; init = copy mol1<br>
&gt; solvatebox init mol2 4<br>
&gt; solvatebox init mol1 2<br>
&gt; saveamberparm init iobox.top iobox.crd<br>
<br>Then equilibrate the box with constant pressure, convert to pdb, and<br>
<br>&gt; solbox = loadpdb solbox.pdb<br>
&gt; solvatebox mymol solbox 10<br>
<br>Or you could build up the layers directly around your solute, then put a<br>
cartestian restraint on the solute while equilibrating it (as would also be<br>
necessary if using an intermediate box to solvate the solute).<br>
<br>Likely it will be tricky to get 1:1 ionic ratio, but this will not matter so<br>
much if you are making an ion-only box to then solvate another molecule,<br>
since arbitrary adjustments will still be needed after solvating the other<br>
molecule because of losing the ionic balance. The adjustments can be made by<br>
editing the system in xleap and deleting extra solute molecules of the<br>
appropriate species.<br>
<br>You might want to consider debugging your solvent molecules by first running<br>
each separately with Na+ and Cl- to neutralize.<br>
<br>Bill<br>
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Received on Tue May 04 2010 - 14:00:03 PDT
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