Re: [AMBER] How to make ionic liquid solvent box? from Jason Swails on 2010-05-04 (Amber Archive May 2010)

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 4 May 2010 18:10:00 -0400

Hello,

All I got was garbled mark-up language. Can you try using default, ASCII
emails without any markup so we can read it more easily? I'm guessing I
won't be the only person with this issue.

All the best,
Jason

2010/5/4 Hoshin Kim <heisen85.hanmail.net>

> <html><head><style> p {margin-top:0px;margin-bottom:0px;} </style></head>
> <body><div style="font-size:12px; font-family:굴림,굴림체,Gulim,Baekmuk
> Dotum,Undotum,Apple Gothic,Latin font,sans-serif;">
> <table border=0 width=100% style='background: transparent;' cellpadding=0
> cellspacing=0 align=center>
> <tr>
> <td valign=top style='padding:8pt;'>
> <div style="color: rgb(51, 51, 51); font-family: 돋움; font-size: 10pt;
> background-color: transparent; line-height: 1.5; padding-top: 8px;
> padding-right: 8px; padding-bottom: 8px; padding-left: 8px; ">
>
> <div style="font-size:12px; font-family:굴림,굴림체,Gulim,Baekmuk
> Dotum,Undotum,Apple Gothic,Latin font,sans-serif;">
> <table border="0" width="100%" style="background: transparent;"
> cellpadding="0" cellspacing="0" align="center">
> <tbody><tr>
> <td valign="top" style="padding:8pt;">
> <div style="color: rgb(51, 51, 51); font-family: 돋움; font-size: 10pt;
> background-color: transparent; line-height: 1.5; padding-top: 8px;
> padding-right: 8px; padding-bottom: 8px; padding-left: 8px; ">
>   font-family: arial, sans-serif; line-height: normal; border-collapse:
> collapse; ">Dear Bill,
> arial, sans-serif; line-height: normal; border-collapse: collapse; "> 
>  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 
> 
> _______________________________________________ 
> AMBER mailing list 
> <a href="mailto:AMBER.ambermd.org" style="color: rgb(0, 84, 136); ">
> AMBER.ambermd.org</a> 
> <a href="http://lists.ambermd.org/mailman/listinfo/amber" target="_blank"
> style="color: rgb(0, 84, 136); ">http://lists.ambermd.org/
> mailman/listinfo/amber</a> 
> </div>
> </td></tr>
> </tbody></table>
> </div>
>
>
>
>
>
>
>
>
> <a href="
> http://www.182.go.kr/child/nSearchFormRead.jsp?flag=1&menu=3|1&DOCID=00167236<http://www.182.go.kr/child/nSearchFormRead.jsp?flag=1&menu=3%7C1&DOCID=00167236>"
> target="_blank"><img src="
> http://mimg.daum-img.net/missingchild/100226_jdh.jpg" width="411"
> height="105" alt="미아찾기 캠페인"
> style="clear:both;margin-top:10px;margin-bottom:20px;border:0px none;"></a>
>
>
> </div></td></tr>
> </table></div></body></html>
>
>
> 
>
> <a href="mailto:heisen85.hanmail.net"><img
> src="http://nametag.hanmail.net/._FcsUoHOnFifuu-PmFirA3tpi2yRqC8"
> border="0"></a>
> 
>
>
>
> 
> <table width="100%" cellspacing="0" cellpadding="0" background="
> http://mimg.daum-img.net/08mail/bg_dot.gif"
> style="margin-top:15px;background-repeat:repeat-x;background-position:left
> top;">
> <tr height="36">
> <td align="left" height="36"
> style="padding-left:5px;font-size:12px;font-family:굴림,gulim,Apple
> Gothic,sans-serif;color:#333333;">
>
> <a href="
> http://allim.daum.net/servlet/Redirect?sid=culturehall_100422_fanta"
> target="_blank"><img height="27" width="266" src="
> http://mimg.daum-img.net/10mail/banner/100408_01.gif" border="0"></a>
>
> </td>
> <td align="right" height="36"
> style="font-size:12px;font-family:굴림,gulim,Apple
> Gothic,sans-serif;color:#333333;">
> <a href="
> http://search.daum.net/search?w=tot&t__nil_searchbox=btn&nil_id=tot&stype=tot&q=%40%BF%B5%C8%AD%BF%AD%C7%F7%C8%B8%BF%F8"
> style="font-weight:normal;font-size:12px;color:#3851c5;font-family:굴림,gulim,Apple
> Gothic,sans-serif;text-decoration:none;" target="_blank"><img src="
> http://mailimg.hanmail.net/10mail/banner/movie_bn_footer_0122.gif"
> width="293" height="27" alt="" border="0" /></a> 
> </td>
> </tr>
> </table>
>
>
> 
>
> <a href='
> http://www.182.go.kr/child/nSearchFormRead.jsp?flag=1&menu=3|1&DOCID=00167236<http://www.182.go.kr/child/nSearchFormRead.jsp?flag=1&menu=3%7C1&DOCID=00167236>'
> target='_blank' ><img src='
> http://mimg.daum-img.net/missingchild/100226_jdh.jpg' width='411'
> height='105' alt='미아찾기 캠페인'
> style='clear:both;margin-top:10px;margin-bottom:20px;border:0px none;'
> /></a>
>
> <img src="
> http://wwl401.hanmail.net:4280/.from=heisen85&rcpt=amber%40ambermd%2Eorg&msgid=%3C20100505060639%2EHM%2E000000000000qux%40heisen85%2Ewwl401%2Ehanmail%2Enet%3E
> ">
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>

-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue May 04 2010 - 15:30:03 PDT