[gmx-users] is it possible to convert NAMD psf file to gromacas format?

[Francesco Oteri]

You can solve the problem without converting from namd to gromacs.
You can use the pdb you've already found to obtain a valid gromacs 
topology through pdb2gmx

Il 29/05/2011 22:24, albert ha scritto:
> Thank you very much for kind messages.
> I am trying to convert a membrane system psf file for gromcas MD 
> simulation. For I would like to use CHARMM36 for my POPC system, but I 
> cannot find pre-equilibrium CAHRMM36 based POPC system. However, there 
> is some for NAMD and I download the pdf and psf file hoping that it 
> could be converted to related gromacs format.
>
> Do you have any idea about this?
>
> THX
>
> At 2011-05-30£¬"Francesco Oteri"<francesco.oteri at gmail.com>  wrote:
>
> >Topology file is suitable for analysis. I succesfully used the .top to
> >analyse hydrogen bond and salt-bridges.
> >I don't know if problems would arise for simulation.
> >
> >
> >Il 29/05/2011 22:10, albert ha scritto:
> >>  Thank you very much for kind advices. Here is some warning, and I
> >>  don't know whether there would be some problem or not:
> >>
> >>  ; 'fake' gromacs topology generated from topotools.
> >>  ; WARNING| the purpose of this topology is to allow using the |WARNING
> >>  ; WARNING| analysis tools from gromacs for non gromacs data. |WARNING
> >>  ; WARNING| it cannot be used for a simulation. |WARNING
> >>
> >>
> >>
> >>  At 2011-05-30£¬"Francesco Oteri"<francesco.oteri at gmail.com>   wrote:
> >>
> >>  >Il 29/05/2011 21:58, albert ha scritto:
> >>  >>   Hello:
> >>  >>   I am wondering, is it possible to convert NAMD topol psf file into
> >>  >>   Gromacs topol format?
> >>  >>
> >>  >>   Thank you very much
> >>  >
> >>  >Hi albert,
> >>  >you can try with the following commands:
> >>  >
> >>  >vmd .psf .pdb
> >>  >topo writegmxtop output.top
> >>  >
> >>  >I recently tried with vmd1.9
> >>  >
> >>  >-- 
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