gurpreet singh wrote:
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.
try
grompp -maxwarn 0
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"
#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
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
Gurpreet
On 7/3/07, *Mark Abraham* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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