[gmx-users] [Fwd: How simulate two peptides in a box?]

gurpreet singh gps.iitm at gmail.com
Wed Jul 4 08:49:24 CEST 2007

Thanks Mark for your advice

 I tried to run the simulation even by removing all the restraints as you
told but the same problem was coming.
In your  second reply you asked me to check the topology file. I have a
doubt in that, actually what are the things i should look at in the topology
file. I have seen my topology file and the related .itp files also but i did
not find anything unusual in that.

Following are the contents of my Topology file:

; Include forcefield parameters
#include "ffG43a1.itp"

; Include chain topologies
#include "aquapomut_grom_A.itp"
#include "aquapomut_grom_B.itp"

; Include water topology
#include "spce.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
SOL                71
CL-                 6
SOL             14825

As i told to last time that my protein is a dimer. so my question is this
problem is becasue of some missing parameter required for  realizing
gromacs that its a dimeric protein?

with regards

On 7/3/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> >  Hello Gromacs users:
> Please don't reply to another user's question with a change of topic and
> not change the subject line of your email. Not doing this means the people
> who might know the answer for you have no idea in advance what you're
> going to be asking, and might not bother reading. Best is to start with a
> new email, not a reply, and to use your subject line sensibly.
> > I am running a  dimeric protein simulation on Gromacs 3.3 using the
> force
> > filed G43a1.
> >
> >
> > For initially minimizing the hydrogen i did some small minimization and
> > equilibration in the vacuum by maintaining the restraints
> > then i added ions and water but in the very first minimization i m
> getting
> > the following error
> If you want to keep your credibility, when people have already made a
> suggestion about how to solve your problem, such as I did here
> http://www.gromacs.org/pipermail/gmx-users/2007-June/028301.html, when you
> post the same problem, you should say what happened when you tried their
> suggestion. They didn't suggest it for their own entertainment.
> Look at the minimization "trajectory" and see where things are breaking.
> Have a look at your topology there, read chapter five thoroughly.
> Mark
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