Introduction

Topology and parameter files to run MD simulation with non-natural sidechains with the CHARMM22 force-field (MacKerell, Jr. et al., Journal of Physical Chemistry B, 1998, 102, 3586-3616) are provided below.
Parameters that could not be infered from the existing CHARMM force-field have been derived from MMFF using SwissParam [Zoete et al, J.Comp.Chem., (2011)].

For general information about CHARMM, please refer to http://www.charmm.org/.

Installation

• Use the new topology file top_all22_prot_swisssidechain.inp.zip, instead of the usual top_all22_prot.inp.
• Add the new parameters from par_all22_prot_swisssidechain.inp.zip to the original ones.

Example:

SET lib PATH_TO_CHARMM_TOPPAR

!------ Topology
open unit 1 card read name @lib/top_all22_prot_swisssidechain.inp
read RTF card unit 1
close unit 1


!------ Parameters
open unit 1 card read name @lib/par_all22_prot.inp
read PARA card unit 1
close unit 1

open unit 1 card read name @lib/par_all22_prot_swisssidechain.inp
read PARA card unit 1 append
close unit 1

D-amino acids

If you have several D-amino acids that are present in SwissSidecain in your structure, you can add this topology file after declaring the top_all22_prot_swisssidechain.inp in your CHARMM imput file:

open unit 1 card read name @lib/top_all22_prot_D_swisssidechain.inp
read RTF card unit 1 append
close unit 1