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

[Mark Abraham]

On 05/30/2011 04:12 PM, albert wrote:
> Thank you very much for your kind reply.
> The problem is that there are too many atom names for 72 full atom 
> lips and it can make mistakes easily.

Hence, writing a script.

> If a rename atom A into B, it will mix the old atom B which already 
> there before A renamed into B. However, if the old atom B also need to 
> be renamed into C. Here is the problem , command cannot recognize this 
> atom B is the new generated or the old atom B. Of course, those atom B 
> derive from A should not be renamed into C.....

Do two passes of sed per the earlier suggestion. Do B->C, then A->B.

> If there is only dozens of atoms name, it would be ok modify them 
> manually. But if there are thousands, it would be a big problem to do so.

This is why you write a sed script, so that there are no errors, and you 
have the script later to document and repeat what you did.

Mark

>
> THX
>
> At 2011-05-30£¬"Francesco Oteri"<francesco.oteri at gmail.com>  wrote:
>
> >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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