Thank you for your help, Mr.Kirschner. I was actually inquiring about a
method wherein, for a given mdin input file in amber-md, what will be the
corresponding ".mdp" file in gromacs, keeping in mind that I want to use
amber-forcefield in both the softwares.
On Mon, May 6, 2019 at 4:03 PM Karl Kirschner <k.n.kirschner.gmail.com>
wrote:
> Hello Akshay,
>
> There is a very nice tool called ACPYPE, written by Alan W Sousa da Silva
> and Wim F Vranken [1]. You can download it at
> https://github.com/alanwilter/acpype . We have recently ensured that 1-4
> scaling is correctly done within this tool, meaning that Glycam06 is now
> converted correctly [2] in addition to the other Amber force fields. We did
> an extensive study to ensure that the parameters generate molecular
> mechanics and MD observables that are essentially the same (i.e. within a
> very small error) for a given Amber leap topology file is used in Amber and
> when converted and used in Gromacs.
>
> 1. SOUSA DA SILVA, A. W. & VRANKEN, W. F. ACPYPE - AnteChamber PYthon
> Parser interfacE. BMC Research Notes 2012, 5:367
> doi:10.1186/1756-0500-5-367 http://www.biomedcentral.com/1756-0500/5/367
>
> 2. Austen Bernardi, Roland Faller, Dirk Reith and Karl N. Kirschner, ACPYPE
> update for Nonuniform 1--4 Scale Factors: Conversion of the GLYCAM06 Force
> Field from AMBER to GROMACS, SoftwareX, accepted on April 25, 2019.
>
> Bests,
> Karl
>
> On Mon, May 6, 2019 at 11:59 AM Akshay Prabhakant <
> akshayresearch16.gmail.com> wrote:
>
> > Just like this page <http://ambermd.org/namd/namd_amber.html>, which
> shows
> > conversion of amber-md input-parameter values into equivalent values for
> > namd-input file, can anyone suggest me a way of converting amber-md
> > input-parameters to gromacs-md input-paramters(using amber forcefield)?
> > Thanks in advance.
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Received on Mon May 06 2019 - 04:30:02 PDT
