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

[Francesco Oteri]

I guess it is tedious but, in my opinion it is more correct changing the 
atom name in the pdb and using gromacs topology generation tools. So you 
are sure the topology will be suitable for gromacs simulation.

You rename atom, using the command sed.
In particular:

sed "s/old/new/g" file

replaces each occurence of "old" with "new". Once you find the 
correspondenze between gromacs and pdb atom name, you can solve the 
problem.


Alternatively,you can replace atom name using some text file editor.




Il 29/05/2011 22:35, albert ha scritto:
> Well, I also try to do this. But it seem that the atom name in my POPC 
> pdb file (which I download from here 
> http://terpconnect.umd.edu/~jbklauda/research/download.html ) is 
> different from the the one in Gromacs topol database. There are 72 
> lips in the system in all. So, it would be very difficult to modify 
> them one by one.
>
> Thank you very much
>
> At 2011-05-30£¬"Francesco Oteri"<francesco.oteri at gmail.com>  wrote:
>
> >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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