Thanks for your help.
JunBeom
2020년 1월 9일 (목) 오후 5:03, David Cerutti <dscerutti.gmail.com>님이 작성:
> OK, it looks like you are already trying to add extra points to your
> molecules. In peo.prepin, I see this:
>
> 0 0 2
> This is a remark line
> peo.res
> PEO INT 0
> CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.523 111.21 .0 .00000
> 4 C1 c3 M 3 2 1 1.540 111.208 -180.000 0.000000
> 5 H1 h1 E 4 3 2 1.094 72.659 67.710 0.000000
> 6 H2 h1 E 4 3 2 1.094 68.999 -173.703 0.000000
> 7 O1 os M 4 3 2 1.421 179.004 -111.371 0.000000
> 8 EP EP E 7 4 3 1.274 101.287 21.028 0.000000
> 9 EP EP E 7 4 3 1.186 82.628 22.345 0.000000
> 10 C2 c3 M 7 4 3 1.422 111.502 -0.924 0.000000
> 11 H4 h1 E 10 7 4 1.094 108.415 -179.974 0.000000
> 12 H5 h1 E 10 7 4 1.094 110.502 61.094 0.000000
>
> LOOP
> IMPROPER
> DONE
> STOP
>
> That is nearly correct. You need to modify the lines for atoms 8 and 9 to
> read more like this:
>
> 8 EP1 EP E 7 4 3 0.700 120.000 180.000 0.000000
> 9 EP2 EP E 7 4 3 0.700 120.000 0.000 0.000000
>
> You need to name your EPs in the second column, but the atom types in the
> third column are correct. The connectivity numbers you've got look right--
> E 7 4 3 means "chain terminating, bond to atom 7, make angle with -7-4, and
> make dihedral with -7-4-3." Then you need to give proper bond, angle, and
> dihedral values for the -7, -7-4, and -7-4-3 arrangements. The numbers
> I've given will make 0.7A bonds between the O1 oxygen and the EPs, 120
> degree angles (what else would you want for sp2 lone pairs?), and then put
> them cis and trans to the C1 atom so you get them on opposite lobes of the
> O1. The last number is the charge field, but I assume you're going to fit
> charges somehow.
>
> If you want to fit your own charges, mdgx has a nice facility for fitting
> EP charges of the sort you're trying to make, but I have not used it much
> in this particular capacity.
>
> Dave
>
>
> On Tue, Jan 7, 2020 at 4:05 AM 조준범 <j1300704.gmail.com> wrote:
>
> > .ac files and .prepi files are included.
> > If you have any problem, please let me know.
> >
> > I think I made polymer properly, but I don't have any idea how to make
> > multiple chains with already built polymer and insert polymers into other
> > systems.
> >
> > For example, adding polymers (configuration A) into ionic liquids
> > (configuration B)
> >
> > I've tried to combine polymers and ionic liquids.
> > First, I used packmol to make PEO-IL.pdb.
> > Then, I used tleap again to make .prmtop file.
> > tleap commands are below.
> >
> > source leaprc.gaff
> > source leaprc.water.spce
> > source leaprc.GLYCAM_06EPb
> >
> > set default IPOL 1
> >
> > TFS = loadmol2 tfsi.mol2
> > RTIL = loadPdb RTIL.pdb
> >
> > loadamberparams frcmod.tfsi
> > loadamberparams frcmod.ions1lm_1264_spce
> >
> > addIons RTIL LI 10
> >
> > saveAmberParmPol RTIL RTIL.prmtop RTIL.inpcrd
> >
> > And if I want to change polarizability of atoms which is consist of PEO,
> > how can I manipulate?
> >
> > Thank you in advance.
> >
> > 2020년 1월 7일 (화) 오후 4:57, David Cerutti <dscerutti.gmail.com>님이 작성:
> >
> > > The way to do this is somewhat involved for a beginner. I have done it
> > > manually, and you can do it in the current Amber release. What you
> will
> > > need to do is get a prepin format file for your molecule (antechamber
> > > output) and then add lines manually for the EP atoms. This will take
> > some
> > > modifications of the connectivity. If you can send me your prepin file
> > it
> > > might be the easiest thing. I can tell you then what I did so you see
> > how
> > > to do it for yourself. I just got contracted to integrate a more
> diverse
> > > EP functionality into pmemd, so in time this capability will filter
> down
> > to
> > > standard users through standard channels like tleap.
> > >
> > > Dave
> > >
> > >
> > > On Tue, Jan 7, 2020 at 1:41 AM 조준범 <j1300704.gmail.com> wrote:
> > >
> > > > Hi all,
> > > >
> > > > I'm working on poly(ethylene oxide) with ionic liquid system.
> > > > And now I'm trying to make peo with 2 extra points on oxygen atoms.
> > > >
> > > > I can make polymer without extra points, which is explained at
> tutorial
> > > > site. But I have no idea how to attach extra points.
> > > >
> > > > Are there any site or examples I can refer to?
> > > >
> > > > Any advice would be grateful.
> > > >
> > > > --
> > > >
> > > > *Junbeom Cho*
> > > >
> > > > Integrated Ph. D. Student
> > > >
> > > >
> > > >
> > > > Theoretical and Computational Soft Matters Laboratory
> > > >
> > > > School of Chemical and Biological Engineering
> > > >
> > > > Seoul National University
> > > >
> > > > 1, Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
> > > >
> > > >
> > > >
> > > > Tel: +82-2-880-1529
> > > >
> > > > E-mail: cjb0704.snu.ac.kr
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> >
> > *Junbeom Cho*
> >
> > Integrated Ph. D. Student
> >
> >
> >
> > Theoretical and Computational Soft Matters Laboratory
> >
> > School of Chemical and Biological Engineering
> >
> > Seoul National University
> >
> > 1, Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
> >
> >
> >
> > Tel: +82-2-880-1529
> >
> > E-mail: cjb0704.snu.ac.kr
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Junbeom Cho*
Integrated Ph. D. Student
Theoretical and Computational Soft Matters Laboratory
School of Chemical and Biological Engineering
Seoul National University
1, Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
Tel: +82-2-880-1529
E-mail: cjb0704.snu.ac.kr
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Received on Thu Jan 09 2020 - 21:30:02 PST
