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5 Introductory Case Studies
 

(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2005

5.5 Case Study - Folding TRP Cage (Advanced analysis and clustering) - SECTION 2

By Ross Walker

Stage 2: Creating the prmtop and rst7 files.

Now that we have the structure, we can create our prmtop and rst7 files. Before we do this we should ensure we are using the same parameters and simulation settings as they used in the paper. Paragraph 3 reads:

    We initiated our simulations using only the trpcage TC5b2 amino acid sequence (N20LYIQWLKDGGPSSGRPPPS39), with an extended initial conformation built by the LEaP module of AMBER version 6.0.4 All molecular dynamics (MD) simulations were fully unrestrained and carried out in the canonical ensemble using the SANDER module, which we modified to improve performance on the Linux/Intel PC cluster that was used for all calculations. The ff99 force field5 was employed, with the exception of [phi/psi] dihedral parameters which were refit6 (see Supporting Information) to improve agreement with ab initio relative energies7 of alanine tetrapeptide conformations. Parameters were not fit to data for the trpcage. Solvation effects were incorporated using the Generalized Born model,8 as implemented9 in AMBER.

So, they first built a linear structure in xleap, which we have just done. Then they performed unrestrained MD simulations at constant temperature (canonical ensemble) in an implicit Generalised Born solvent. AMBER supports a number of different generalised Born models, the most advanced at the time of writing is the modified GB model developed by A. Onufriev, D. Bashford and D.A. Case using the model II radii (IGB=5) as described in the paper referenced in the GB section of the AMBER manual. In the paper they don't specify the specific GB model that was used but this is most likely because only IGB=1 was available when they carried out this research. In order to try and ensure our simulation protocol is as close as possible to that in the paper we will stick to IGB=1. The default radii used by LEaP are compatible with IGB=1 so we don't need to specify what radii set to use.

They also note that they used the FF99 force field as we plan to, but with modified phi/psi dihedral parameters. These parameters are a correction to the FF99 phi/psi parameters that tended to overly favour alpha-helix structures. In order to reproduce the results in the paper it is essential to include these changes when building our prmtop file. Unfortunately the supplemental info in this paper does not make it immediately obvious what parameters have been changed. They simply give a copy of the modified parm99.dat file. This I believe was due to the fact that AMBER 6 did not ship with the FF99 force field, it was added later. As such at the time there were several copies floating around which had various typos etc. By reproducing the whole parm99.dat file in the paper the authors ensured that people saw that they were using the official FF99 force field. Unfortunately ACS give this data as a pdf, rather than a text file, which makes it exceptionally hard to extract in usable form. Fortunately these modifications are included in the AMBER8 distribution in the directory $AMBERHOME/dat/leap/parm/ as frcmod.mod_phipsi.1. In Amber 9 this modification has been removed since it causes problems with glycine parameterization. It has been essentially replaced by a more in-depth reparameterization of FF99 referred to as FF99SB. If you are considering your own simulations you would be advised to use FF99SB instead of the mod_phipsi.1 modifications. However, our goal here is a reproduction of the simulations in the JACS paper where the authors used mod_phipsi.1 so we will do the same. For Amber 9 users I have included a link to this file below.

frcmod.mod_phipsi.1
from Simmerling, Strockbine, Roitberg, JACS 124:11258, 2002. Modifies parm99.
MASS

BOND

ANGL

DIHEDRAL
N -CT-C -N 1 0.700 180.000 -1.
N -CT-C -N 1 1.100 180.000 2.
C -N -CT-C 1 1.000 0.000 1.

NONB

As you can see, only 3 dihedral parameters have been changed. So we can simply load this file into xleap and it will overwrite the relevant parameters. So, if you closed xleap, re-open it and load the structure back in:

    $AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/oldff/leaprc.ff99
    >loadoff TC5b_linear.lib

Now load the replacement dihedral parameters:

    >loadamberparams frcmod.mod_phipsi.1

We can now save our prmtop and rst7 files:

    >saveamberparm TC5b TC5b.prmtop TC5b.rst7

Here are the files: TC5b.prmtop, TC5b.rst7


CLICK HERE TO GO TO SECTION 3


(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2005