[gmx-users] Porting to Gromacs of Parmbsc1

[Alan]

Did you try to generate the whole system (with water and ions) in Tleap?
Then export the amber param and coord files and use acpype to convert the
whole system to GMX. Acpype try to guess the solvent, but it even has this
option:

  -u, --direct          for 'amb2gmx' mode, does a direct conversion, for
any
                        solvent

case you have the most awkward solvent in Amber.

On 5 July 2016 at 10:45, 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).
>
> 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". So I
> tried to include manually the water model on the topology, but then I get
> errors like "Atom type ow_... not defined".
>
> 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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-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588