[gmx-users] Porting to Gromacs of Parmbsc1

[Mark Abraham]

Hi,

On Tue, Jul 5, 2016 at 1:20 PM Elisa <elisa.dellano.fl at ait.ac.at> wrote:

> Mark Abraham <mark.j.abraham at ...> writes:
>
> >
> > Hi,
> >
> > Not to my knowledge, but at the page you linked, BSC recommends using
> > AmberTools and ACPYPE...
> >
> > Mark
> >
> > On Mon, 15 Feb 2016 15:18 Sarath Chandra <sarathchandradantu at ...>
> > wrote:
> >
> > > A forcefield on Parmbsc1 is out and it has reportedly fixed some issues
> > > with DNA structures
> > >
> > > http://www.nature.com/nmeth/journal/v13/n1/full/nmeth.3658.html
> > > http://mmb.irbbarcelona.org/ParmBSC1/help.php?id=download
> > >
> > > Is there a script to convert lib and frcmod files to a newFF.ff
> directory
> > > and then check the forcefield for validation?
> > >
> > > Regards,
> > >
> > > Sarath
> > >
> > >
> > >
> > >
> > >
> > > Validating would be running some test systems
> > >
> > > On 14 February 2016 at 20:24, Mark Abraham <mark.j.abraham at ...>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > Nobody's working on it to my knowledge, but if a forcefield has been
> > > > published, seems likely to be of use to multiple people, and a
> validation
> > > > script can show it works correctly with respect to the reference
> > > > implementation, then we'll consider it for inclusion in GROMACS.
> > > >
> > > > Mark
> > > >
> > > > On Sun, 14 Feb 2016 14:39 Sarath Chandra <sarathchandradantu at ...>
> > > > wrote:
> > > >
> > > > > I wish to use Parmbsc1 for DNA simulations. Are there any
> timelines to
> > > > port
> > > > > Parmbsc1 into Gromacs along with amber14sb?
> > > > >
> > > > > Regards,
> > > > >
> > > > > Sarath
> > > > > --
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>
> Hello everyone,
>
> Sorry for reviving this topic. I'm also interested in getting ParmBSC1 to
> work with Gromacs. So far I have tried several approaches.
>
> The first one was, as the instructions on ParmBSC1's website state, to load
> all fields in Leap using AmberTools 14, then I loaded my structure, I add
> ions and solvate (also tried solvating first and adding ions later), and
> then used ACPYPE to get the Gromacs files. This doesn't work for me (I used
> 1bna from the PDB), at the energy minimization step the system blows up
> (very likely is because of water molecules overlapping).
>

Well, you could prove it and then find out how to fix it :-) Look at the
coordinate files you have at various stages and see where something is
doubtful.

Alternatively, use acpype to convert the topology twice, with and without
the extra stuff. Then use the unsolvated coordinate file to generate
solvent and ions using GROMACS tools. Then combine the resulting coordinate
file with the solvated topology file, adjusting numbers of molecules in the
[ system ] field appropriately. But first learn how to use these tools when
you have a standard force field...

Another approach I followed was to load everything on Amber and export to
> Gromacs with ACPYPE before solvating and adding ions. Then I tried to
> generate the box in gromacs but I got the error "No type SOL defined".


It's kinda hard to help without seeing your commands used...


> So I
> tried to include manually the water model on the topology, but then I get
> errors like "Atom type ow_... not defined".
>

If the force field requires a custom water, then yes, you need to import
its atom types as well.

Mark

So at this point I am looking for:
> - Either a way to remove overlapping waters or to understand if they are
> coming from amber or it is an ACPYPE problem.
> - A way to incorporate the ions and solvent in Gromacs while using the
> topology generated with ACPYPE.
> - Or the ParmBSC1 field in gromacs or how to export it to gromacs.
>
> Am new to MD simulations, just started two months ago, so any information
> or
> help I can get I will appreciate it.
>
> Thank you!
>
>
>
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