# Re: [AMBER] [ Polymer with Extra Points ]

From: David Cerutti <dscerutti.gmail.com>
Date: Thu, 9 Jan 2020 03:02:47 -0500

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

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
>
>
>
>
> saveAmberParmPol RTIL RTIL.prmtop RTIL.inpcrd
>
> And if I want to change polarizability of atoms which is consist of PEO,
> how can I manipulate?
>
>
> 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
>
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Received on Thu Jan 09 2020 - 00:30:02 PST
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