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

[Jianguo Li]

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
>G >> >>  >>   ; 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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