.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
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Received on Tue Jan 07 2020 - 01:30:02 PST
