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

[Francesco Oteri]

Il 30/05/2011 08:32, Mark Abraham ha scritto:
> 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.....
>

You can use vmd to do this.
For example, to rename C-alpha as C-beta, and C-beta as C-alpha, you 
have to use the following commands:

set sel1 [atomselect top "name CB"]
set sel2 [atomselect top "name CA"]
$sel1 set name CA
$sel2 set name CB


It is important selecting the atoms before renaming them. After, you can 
replace the atomic name without confusion.
The above approach can be used to write a vmd script and, in turn, this 
permit you to build your initial model starting from scratch.
Further, it permits you to remember the steps you are doing to build the 
starting structure without using your own neurons to store the 
informations :)




> 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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