[gmx-users] (no subject)

[Fernando Mattio]

 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"

; 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
> >
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20051010/36e83543/attachment.html>