[gmx-users] (no subject)

[Alan Dodd]

This is common for multi-chain topologies I think, the
main .top has links within it for each chain, which
then contain all the required info for each chain.

--- Fernando Mattio <mattiofer at gmail.com> wrote:

>  Dear gromacs users,
> Well I looked at my created topology file and it was
> like this:
> 
> 
> ;
> ; File 'minimized_2water.top' was generated
> ; By user: simulant (1000)
> ; On host: lvt-uni-e09-3
> ; At date: Fri Oct 7 13:47:39 2005
> ;
> ; This is your topology file
> ; LYSOZYME
> ;
> ; Include forcefield parameters
> #include "ffG43a1.itp"
> 
> ; Include chain topologies
> #include "minimized_2water_A.itp"
> #include "minimized_2water_B.itp"



This bit above is where all the protein info is
stored.
You shouldn't have to do anything special, as long as
the two .itp files above are somewhere accessible -
either in share/top or where you're running the
programs.



> 
> ; Include water topology
> #include "spc.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
> 
> ; Include generic topology for ions
> #include "ions.itp"
> 
> [ system ]
> ; Name
> LYSOZYME
> 
> [ molecules ]
> ; Compound #mols
> Protein_A 1
> Protein_B 1
> SOL 10017
> SOL 10017
> 
> 
> A topology file should be a lot bigger, at least it
> was what I realized
> looking to the topology of my protein(aki.top). So
> shouldn´t be there also
> the informations about my protein?? I mean, what do
> I have to do with this
> "part" of topology created, should I include this to
> my other topology file
> (aki.top)? Any help would be greateful, as I wrote
> before I am a new user,
> it´s the first time that I try to do this, I mean,
> to update a topology
> file.
> Thank you very much in advance!
> Fernando Mattio
> 
> 2005/10/7, Fernando Mattio <mattiofer at gmail.com>:
> >
> > Thank you Elena,
> > I think the topology was updated, but I had
> problems related to "Memory
> > access error" when i used the mdrun to perform the
> simulation... So I was
> > wondering if it is not enough memory of my
> computer or if I should have
> > somehow updated also the parameter file... Please
> gromacs users any
> > information about would be great,
> > Thanks in advance,
> > Fernando Mattio.
> >
> > 2005/10/7, elena.papaleo
> <elena.papaleo at unimib.it>:
> > >
> > > Dear Fernando,
> > > I think you can use the command pdb2gmx -f
> > > minimized_2water.gro -p minimized_2water.top
> > > to update your topology file...
> > > best regard
> > > Elena Papaleo
> > >
> > >
> > > Elena Papaleo, PhD Student
> > > Department of Biotechnology and Biosciences
> > > University of Milano-Bicocca
> > > P.zza della Scienza 2, 20126 Milano (Italy)
> > >
> > > email: elena.papaleo at unimib.it
> > > phone: +39 0264483475
> > >
> >
> >
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