Thank you so much for your kind helps. did you pre-equilibrium it?<br><br>At 2011-05-30,"Jianguo Li" <ljggmx@yahoo.com.sg> wrote:<br> <BLOCKQUOTE id="isReplyContent" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Hi Albert,<br><br>Here is one gro file of 128 POPC lipids which I constructed before using CHARMM36 FF. please check if it is correct before using it. <br><br>Jianguo<br> <br></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> albert <<A href="mailto:leuven@yeah.net">leuven@yeah.net</A>><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <<A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><br><b><span style="font-weight: bold;">Sent:</span></b> Monday, 30 May 2011 14:12:19<br><b><span style="font-weight: bold;">Subject:</span></b> Re:Re: [gmx-users] is it possible to convert NAMD psf file to
gromacas format?<br></font><br>Thank you very much for your kind reply.<br>The problem is that there are too many atom names for 72 full atom lips and it can make mistakes easily.<br>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..... <br><br>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. <br><br><br>THX<br><div></div><br><pre><br><span>At 2011-05-30,"Francesco Oteri" <francesco.oteri> 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
>> <a target="_blank" href="http://terpconnect.umd.edu/%7Ejbklauda/research/download.html">http://terpconnect.umd.edu/~jbklauda/research/download.html</a> ) 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> 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> 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> 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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>> >> >
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>
>--
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>Please search the archive at <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!
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</francesco.oteri></francesco.oteri></francesco.oteri></francesco.oteri></span></pre></div></div>
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