Hello everyone,
Thank you Erdem for the suggestions.
>Each missing parameter may cause the molecule to move away from real
life and decrease your force field quality. I think, Before giving a
clear
answer, it would be right to perform pre-tests and make a decision
according to the results of the tests.
>>> I am currently focusing on one isomer and get results. Later I will
perform multiconfigurational fitting and compare the results. Is it the
"perform pre-tests" you mean?
Regards
Ranajit
----- Original Message -----
From: "Erdem Yeler" <erdemyeler.gmail.com>
Sent Date: 04:27:39 Wed April 13, 2022
> >Do I have to use all of these conformations, which seem to be a
little
> harder for me?
> >>>Each missing parameter may cause the molecule to move away from
real
> life and decrease your force field quality. I think, Before giving a
clear
> answer, it would be right to perform pre-tests and make a decision
> according to the results of the tests.
>
> <rsaha.icredd.hokudai.ac.jp> adresine sahip kullanıcı 11 Nis 2022 Pzt,
> 06:00 tarihinde şunu yazdı:
>
> > Hello Everyone,
> >
> > I am new to amber (and in molecular dynamics simulation too). My
final
> > goal is to generate an amber force field for the monomer of a
polymer
> > and use them in the GROMACS.
> >
> > █ I have been studing a few tutorials about the generation of amber
> > force field and I get a few points that I need to clear for myself.
I
> > will write them below. If I get some comments and suggestions, it
will
> > be very beneficial to me.
> >
> > (1) One isomer case: If there is only one isomer exists, direct .AC
(
> > antechamber) can be generated via the g16-esp calculation and resp
> > fitting.
> > (2) More than one isomer: If there exists more than one isomer(s)
which
> > is(are) generated by rotations around single bonds, all of the
isomers
> > should be used in the g16-esp calculations and should be given equal
> > weightage in resp fitting.
> >
> > Please let me know if I am wrong in understanding this two cases.
> >
> > █ For My system, The monomer unit is extended and conjugated
> > polyaromatic hydrocarbon which has two -OH and two -C10 (hydrocarbon
> > chain) as side groups. The rotation around C-C-O-H can generate two
> > different rotamers (within 1.5 kcal/mol range, HF/6-31g(d,p)). The -
C10
> > (hydrocarbon chain) can have a lot of orientations and hence a lot
of
> > isomers to handle.
> >
> > Do I have to use all of these conformations, which seem to be a
little
> > harder for me?
> >
> > Please pardon me for writing this long email.
> > Thank you for your time and for reading this long email.
> > Any suggestion and comment is expected.
> >
> > Regards
> > Ranajit
> >
> > P.S. If someone has any tutorial on generation of force field of
polymer
> > systems and doing the MD, please suggest me. I would like to read it
and
> > follow the steps.
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Apr 14 2022 - 18:30:03 PDT
