AMBER Archive (2008)

Subject: AMBER: Si parameters for MD (AMBER9)

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Fri Apr 25 2008 - 17:08:44 CDT

thank you for the answer
but i need a little more information.

is it possible to use Antechamber to generate parameters for Silica? i
should mention that the surface will not move during the simulation, it
will be fixed.

many weeks ago Scott Brozell wrote some of these parameters, can i copy
them in a file and use that? or am i completely off. I recall a tutorial
that covered creating new parameters but my memory fails me as to where
that tutorial was.

Many thanks,
Taufik

DOCK Amber Score Tetrahedrally Bonded Silicon
MASS
Si 28.085

BOND
ca-Si 323.5 1.513 gaff c3-ca
c3-Si 303.1 1.535 gaff c3-c3
oh-Si 314.1 1.426 gaff c3-oh

ANGLE
ca-ca-Si 63.6 112.47 gaff Si -> c3
ca-Si-c3 62.5 114.61 gaff Si -> c3
ca-Si-oh 67.2 112.97 gaff Si -> c3
c3-c3-Si 63.2 110.63 gaff Si -> c3
c3-Si-c3 63.2 110.63 gaff Si -> c3
c3-Si-oh 67.7 109.43 gaff Si -> c3
Si-c3-hc 46.4 110.05 gaff Si -> c3
Si-oh-ho 47.1 108.16 gaff Si -> c3

DIHE
ca-ca-Si-c3 6 0.000 0.000 2.000 gaff X -c3-ca-X
ca-ca-Si-oh 6 0.000 0.000 2.000 gaff X -c3-ca-X
ca-Si-c3-c3 9 1.400 0.000 3.000 gaff X -c3-c3-X
ca-Si-c3-hc 9 1.400 0.000 3.000 gaff X -c3-c3-X
ca-Si-oh-ho 3 0.500 0.000 3.000 gaff X -c3-oh-X
c3-c3-Si-c3 1 0.18 0.0 -3. gaff c3-c3-c3-c3
c4-c3-Si-c3 1 0.25 180.0 -2. gaff c3-c3-c3-c3
c3-c3-Si-c3 1 0.20 180.0 1. gaff c3-c3-c3-c3
c3-c3-Si-oh 9 1.400 0.000 3.000 gaff X -c3-c3-X
c3-Si-c3-hc 1 0.16 0.0 3. gaff Si -> c3
c3-Si-oh-ho 1 0.16 0.0 -3. gaff ho-oh-c3-c3
c3-Si-oh-ho 1 0.25 0.0 1. gaff ho-oh-c3-c3
c3-Si-oh-ho 1 0.25 0.0 1. gaff Si -> c3
oh-Si-c3-hc 1 0.25 0.0 1. gaff Si -> c3

IMPROPER
Si-ca-ca-ca 1.1 180.0 2.0 Using
default value

NONBON
   Si 2.220 0.320 DOCK vdw_AMBER_parm99.defn

David A. Case wrote:
> On Wed, Apr 23, 2008, taufik.alsarraj_at_utoronto.ca wrote:
>
>> I was fortunately able to save a silica slap in mol2 format and i can
>> load it in xleap and view the structure using edit. However i cannot
>> use the command saveamberparm, i get many many errors
>>
>> for atom .. could not find type ...O.3 or Si
>>
>> I am using AMBER9
>> I used leaprc.ff03ua
>
> The standard amber parameters files, like ff03ua, are for proteins and nucleic
> acids. They are not suitable for things like silica. Amber doesn't contain
> force field for silica: you will have to construct your own, or get them from
> the literature.
>
> ...dac
>
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