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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Received on Sun Apr 10 2022 - 20:30:02 PDT
