[gmx-users] is it possible to convert NAMD psf file to gromacas format?
albert
leuven at yeah.net
Mon May 30 09:02:24 CEST 2011
Thank you so much for your such kind helps. I will try it.
At 2011-05-30，"Jianguo Li" <ljggmx at yahoo.com.sg> wrote:
I equilibrated the system for about 20ns at 300K.
Jianguo
From: albert <leuven at yeah.net>
To: Jianguo Li <ljggmx at yahoo.com.sg>
Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, 30 May 2011 14:52:23
Subject: Re:Re: Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?
Thank you so much for your kind helps. did you pre-equilibrium it?
At 2011-05-30，"Jianguo Li" <ljggmx at yahoo.com.sg> wrote:
Hi Albert,
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.
Jianguo
From: albert <leuven at yeah.net>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, 30 May 2011 14:12:19
Subject: Re:Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?
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" 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" 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" 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" 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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