AMBER Archive (2008)

Subject: RE: AMBER: silica slab

From: Steve Spronk (spronk_at_umich.edu)
Date: Wed Feb 06 2008 - 13:01:22 CST

I'm afraid I can't help you much in determining parameters for your Si slab.
Parameter development is not always straightforward, and typically involves
finding a set of parameters that reproduces experimental values. I imagine
that someone, somewhere, has published a forcefield for what you're looking
for, but you may have to dig a little.

But I can tell you that details on the format of the amber files are found
here: http://amber.scripps.edu/formats.html

Good luck!
-Steve

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Arturas Ziemys
Sent: Tuesday, February 05, 2008 1:35 PM
To: amber_at_scripps.edu; case_at_scripps.edu
Subject: Re: AMBER: silica slab

Thanks for a prompt response. I see.

Could you give some general sketch how to parametrize my system. The
point is I'm very new to Amber and I still do not have clear idea about
preparation plan. I know there are FF files in $AMBERHOME/dat/leap/parm.
I suppose I can add my parameter for Si, e.g. 'parm99.dat'. But let me
be clear what I am gonna do:

CT 12.01 0.878 sp3 aliphatic C
  # This is atomtype, mass, ?? what, comment ??

C H HO N NA NB NC N2 NT N2 N3 N* O OH OS P O2
OW-HW 553.0 0.9572 ! TIP3P water
  # Bonds. I need add Si in my case ?
  # This is bind(atomtype-atomtype), force const in kcal/mol (??),
target value, comment

HW-OW-HW 100. 104.52 TIP3P water
  # Angles. Angle type, force const. in kcal/mol (??), target value, comment

CT-S -S -CT 1 3.50 0.0 -2. JCC,7,(1986),230
CT-S -S -CT 1 0.60 0.0 3. JCC,7,(1986),230

# Dihedral. Type, ?? multiplicity , force const, target , ??what,
comment. What are those positive/negative integers in 5th column ?

N NA N2 N* NC NB NT NY
C* CA CB CC CD CK CM CN CQ CR CV CW CY CZ
# What this ?

MOD4 RE
   H 0.6000 0.0157 !Ferguson base pair geom.
   HO 0.0000 0.0000 OPLS Jorgensen,
JACS,110,(1988),1657
   HS 0.6000 0.0157 W. Cornell CH3SH --> CH3OH FEP
   HC 1.4870 0.0157 OPLS
# LJ ??. Type, Rmin (??), epsilon ?

Best
Arturas

David A. Case wrote:
> On Tue, Feb 05, 2008, Arturas Ziemys wrote:
>> I have problems preparing pure Si slab. I have constructed Si slab
>> (crystal), but when I run antechamber i get Error (liek below).
>
> This is not surprising. Amber was developed for molecular simulations
> (primarily for biomolecules), not for crystals. Antechamber only works on
> molecules, and its parameterization is for organic molecules.
>
> I can't think of anyway to use antechamber to develop parameters for Si
slabs,
> and you will probably have to do this "by hand" (or by adapting published
> parameters from other investigators.)
>
> ...dac
>
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