BIGNASim database structure and analysis portal for nucleic acids simulation data

ParmBSC1 forcefield, a refined force-field for the atomistic simulation of DNA.

The set of parameters defined in parmBSC1 forcefield can be found in the download section. Also, instructions to use it with Amber package and Gromacs package are described in the instructions section.

Download files:

ParmBSC1 forcefield consists of two different files:

Library Parameters
Frcmod Parameters

Download ParmBSC1 forcefield parameters

Instructions:

Loading the parmBSC1 force-field using AmberTools14 (free at https://ambermd.org):
----------------------------------------------------------------------------------------------------------------------

  1. Source leaprc.ff14SB, default parm99bsc0 parameters for DNA ($AMBERHOME/dat/leap/cmd/leaprc.ff14SB).

  2. Load parmBSC1.lib, a library that has all DNA nucleotides but having changed the following atom types:

    • atom name C5' is changed from CT to CI (parmbsc0)
    • atom name C3' is changed from CT to CE.
    • atom name C8 is changed from CK to C1 (adenine).
    • atom name C5 and C6 are changed from CM to C2 (thymine).

  3. Load an extra parameters file (parmBSC1.frcmod) that includes all the new parameters needed due to the new atom types definition and the new QM-fitted parameters.

  4. Load the pdb of the structure that you want to simulate.

  5. Perform any additional command (addions, solvate, saveamberparm, etc.).



Example using Ambertools Leap program: 

source $AMBERHOME/dat/leap/cmd/leaprc.ff14SB
addAtomTypes {
  { "C1" "C" "sp2" }
  { "C2" "C" "sp2" }
  { "CI" "C" "sp3" }
  { "CE" "C" "sp3" }
 }
 loadoff parmBSC1.lib
 loadamberparams parmBSC1.frcmod


Loading the parmBSC1 force-field using Gromacs (free at https://www.gromacs.org/):
----------------------------------------------------------------------------------------------------------------------


Two different options exist to use parmBSC1 forcefield with Gromacs package:

The first one, and the recommended, is using the native porting developed by Berg Hess (Gromacs Developer) for Gromacs. It can be found here:

GROMACS Force Fields: User contributions with the name amber99bsc1.ff.tgz

The second one is following the previous steps using Ambertools Leap program, with an additional step:

  1. Perform the 5 steps explained in the previous section (Loading the parmBSC1 force-field using AmberTools14).

  2. Convert topology and coordinate files from Amber to Gromacs format with ACPYPE program (containing a redefinition of amb2gmx.pl).

    3. Example of ACPYPE program usage: 

    
python acpype.py -p example.prmtop -x example.rst
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2015 AWSdS |
============================================================================
Converting Amber input files to Gromacs ...
==> Writing GROMACS files

Total time of execution: 1s

    References: