Re: [AMBER] Parameterization of ffamber99sb for octane box

From: FyD <>
Date: Thu, 09 Dec 2010 08:47:01 +0100

Dear Yuvraj,

> I have to create an octane box for studying effect of solvent hydrophobicity
> on enzyme activation.
> Anyone using octane parameterized file in amber?
> Please suggest me how to parameterize it or is there any tutorial for it.
> As i am a beginner, so plz explain in steps.

By analogy to cyclohexane, see the project W-43 in R.E.DD.B.:

Read the following paper by Williams about MEP-based charges & alkanes

You could follow this approach:
-1 Build a PDB file using xLEaP (you might decide to build several

-2 Use this PDB file as input to generate a P2N file using R.E.D.
Server/Ante_R.E.D. 2.0 (do not
use Ante_R.E.D. 1.x available in the R.E.D. III.4 tools . chemical equivalencing is
not fully determined)
    PDB --> P2N
(concatenate the P2N files corresponding to the different
conformations into a single one if you decided to use different
conformations; see the format .

-3 Use this P2N file as input for R.E.D. Server/R.E.D. IV (or use
R.E.D. III.4) to compute RESP charges in a force field library (mol2
file format)
    P2N --> MOL2

-4 Use tLEaP to add force field atom types (simple since the type of C
is 'CT' and that of H is 'HC') in the mol2 file
OCT = loadmol2 filename.mol2
set OCT name "OCT"
# head & tail not needed since whole molecule
set OCT.1 restype solvent
set OCT.1 name "OCT"
set OCT.1.C1 type CT
set OCT.1.H11 type H1
or simply replace (manual editing) the chemical element the FF atom
type in the mol2 file format

-5 You do not need any frcmod file (for missing force field parameter)

This is quite simple this should take 2 minutes using R.E.D. Server -
a little more if you decide to use different conformations ;-)

regards, Francois

AMBER mailing list
Received on Thu Dec 09 2010 - 00:00:02 PST
Custom Search