Dear all,
I am very new in Amber, and didn't find a propper answer to my problem.
I want to make MD on a small organic molecule containing Si.
(trialkylsilyl group)
I thought on usage GAFF, but there is no parameters for Silicon.
I found
http://archive.ambermd.org/200804/0353.html, but i am badly
confused that as far as i understand parameters simply copied from
carbon. That looks little bit weird for me.
I tried to generate parameters by my own
1) bond length and angles from DFT and MP2 calculations
2) force constants by parmgen. Seems this way they depends only on a
bond length and not on a type of atom, that isn't true generally for
gaff.dat, but ok, they looks not too strange so i accept them.
3) wdv-radii and 6/12 parameter that i found in papers fits to mentioned
on a link (Si 2.220 0.320) and seems i can ignore polarisation.
(I put my parameters at the end of the email)
Nevetherless i have problem with dihedrals.
I tried to follow
http://www.ub.edu/cbdd/?q=content/small-molecule-dihedrals-parametrization
and perform set of Gaussian MP4//MP2 calculations but didn't succed even
with tetramethylsilane molecule (multiple unclear problems with
run_all_sander_param.sh script).
Principally i am doubting very much that i am going right way.
I tried to search answer on
http://q4md-forcefieldtools.org/REDServer-Development/ but the part i
liked the most FFParmDev seems does not exist.
Can anyone provide simple instruction of getting parameters for "missing
elements"?
I do not need high-quality parameters, while i hope that Alk3Si group
will be just a bulky substituent in my calculation.
Thanks in advance.
Dmitriy
BOND c3-Si 172.244 1.934
ANGLE c3-Si-c3 34.106 109.596
ANGLE hc-c3-Si 51.289 105.262
ANGLE c3-c3-Si 73.692 112.904
NONBON Si 2.220 0.320
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Received on Mon Jul 20 2015 - 16:30:03 PDT
