you may need to load frcmod files to get the parameters merged properly -
let us know in more detail what you're trying to do and we can help more.
also, to add what Hannes said, some of the Amber force fields use a
different charge model (such as ff03), and I don't know of extensive tests
checking the compatibility when the charges are derived using different
methods. It may be ok, but I would be more comfortable combining sets that
are the same in that respect. Maybe others on the list know of papers that
reported quantitative testing of the compatibility.
On Thu, Oct 30, 2014 at 5:26 AM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk
> wrote:
> You would first need to make sure that both force fields are compatible
> with each other. If you want to combine two AMBER force fields you
> should be fine.
>
> You will only need to create one single parmtop file with leap as pmemd
> or sander will only read one. Read coordinates for both protein and
> lipids into leap. You may find the 'combine' command to be useful here.
>
> Cheers,
> Hannes.
>
>
> On Thu, 30 Oct 2014 13:15:40 +0530
> Bhushan <nagbiotech1.gmail.com> wrote:
>
> > Hi,
> >
> > I have a query regarding the usage of two different force fields in
> > single simulation, like protein and lipid. I believe both should be
> > assigned with different force fields. In such case how to generate
> > the prmtop file.
> >
> > Do we need to generate two different prmtop files (protein.prmtop and
> > lipid_membrane.prmtop) and then merge them before solvating, or what
> > should I do.
> --
> Scanned by iCritical.
>
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>
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Received on Thu Oct 30 2014 - 08:30:02 PDT
