Step One: Prepare the Topology
The protein we will be working with is the KALP model peptide, denoted KALP15, which has a sequence of: Ac-GKK(LA)4LKKA-NH2. The protocol described here is based on a system built by Kandasamy and Larson in a study of hydrophobic mismatch. The original reference can be found here.
The peptide was prepared in-house using the xLeap module of AmberTools, using ideal backbone geometry of an α-helix (φ = -60°, ψ = -40°). The .pdb file was oriented along the z-axis using editconf -princ, followed by a rotation about the y axis. Note that in GROMACS-3.3.x, the -princ option oriented the long axis of the structure (in this case, the helix axis) along the z-axis by default, but this option has changed as of GROMACS-4.0.4, which orients the long axis along the x-axis. If you want to skip the construction of this peptide, the properly oriented structure can be found here.
Execute pdb2gmx by issuing the following command:
gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc
When prompted, choose the GROMOS96 53A6 parameter set. Choose "None" for the termini; since we have added acetyl and amide capping groups to the N- and C-termini, respectively, we do not want pdb2gmx to build the normal amine and carboxyl groups. Instead, we want pdb2gmx to add connectivity to our capping groups. The -ignh flag tells pdb2gmx to ignore the H atoms in the input. By default, xLeap gave us an all-atom structure (since the AMBER force fields use explicit hydrogen representation). Due to AMBER naming conventions, these H atoms may not have the same nomenclature as those of the GROMOS96 force field. If we tell pdb2gmx to ignore all input H atoms, it will add back only those that it needs.
Now we will need to make some alterations to the topology.
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