DNA & RNA Structure and Helical Parameters Analyses (NAFlex)
----Tutorial 2 -- Global analysis (XCGY)
Tutorial 3 -- Meta-trajectory (XCGY)
Tutorial 4 -- Experimental vs MD analysis
----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.
ParmBSC1 forcefield consists of two different files:
Library ParametersLoading the parmBSC1 force-field using AmberTools14 (free at http://ambermd.org): ----------------------------------------------------------------------------------------------------------------------
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 http://www.gromacs.org/):
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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:
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: