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. 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.....
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. THX At 2011-05-30，"Francesco Oteri" <francesco.ot...@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.ot...@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.ot...@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.ot...@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 >> >> >> > >> >> >> >-- >> >> >> >gmx-users mailing list gmx-users@gromacs.org >> >> >> >http://lists.gromacs.org/mailman/listinfo/gmx-users >> >> >> >Please search the archive at >> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> >> >> >Please don't post (un)subscribe requests to the list. Use the >> >> >> >www interface or send it to gmx-users-requ...@gromacs.org. >> >> >> >Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> > >> >> >-- >> >> >gmx-users mailing list gmx-users@gromacs.org >> >> >http://lists.gromacs.org/mailman/listinfo/gmx-users >> >> >Please search the archive at >> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> >> >Please don't post (un)subscribe requests to the list. Use the >> >> >www interface or send it to gmx-users-requ...@gromacs.org. >> >> >Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> >-- >> >gmx-users mailing list gmx-users@gromacs.org >> >http://lists.gromacs.org/mailman/listinfo/gmx-users >> >Please search the archive at >> >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> >Please don't post (un)subscribe requests to the list. Use the >> >www interface or send it to gmx-users-requ...@gromacs.org. >> >Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >-- >gmx-users mailing list gmx-users@gromacs.org >http://lists.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-requ...@gromacs.org. >Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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