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.<br><br>Thank you very much<br><div></div><br><pre><br>At 2011-05-30£¬"Francesco Oteri" <francesco.oteri@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@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@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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</pre>