Thanks Mark for your advice<br>
<br>
I tried to run the simulation even by removing all the restraints as you told but the same problem was coming. <br>
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. <br>
<br>
Following are the contents of my Topology file:<br>
<br>
; Include forcefield parameters<br>
#include "ffG43a1.itp"<br>
<br>
; Include chain topologies<br>
#include "aquapomut_grom_A.itp"<br>
#include "aquapomut_grom_B.itp"<br>
<br>
; Include water topology<br>
#include "spce.itp"<br>
<br>
#ifdef POSRES_WATER<br>
; Position restraint for each water oxygen<br>
[ position_restraints ]<br>
; i funct
fcx
fcy fcz<br>
1 1
1000
1000 1000<br>
#endif<br>
<br>
; Include generic topology for ions<br>
#include "ions.itp"<br>
<br>
[ system ]<br>
; Name<br>
Protein in water<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Protein_A 1<br>
Protein_B 1<br>
SOL 71<br>
CL- 6<br>
SOL 14825<br>
~<br>
<br>
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? <br>
<br>
with regards<br>
Gurpreet<br>
<br><div><span class="gmail_quote">On 7/3/07, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
> Hello Gromacs users:<br><br>Please don't reply to another user's question with a change of topic and<br>not change the subject line of your email. Not doing this means the people<br>who might know the answer for you have no idea in advance what you're
<br>going to be asking, and might not bother reading. Best is to start with a<br>new email, not a reply, and to use your subject line sensibly.<br><br>> I am running a dimeric protein simulation on Gromacs 3.3 using the force
<br>> filed G43a1.<br>><br>><br>> For initially minimizing the hydrogen i did some small minimization and<br>> equilibration in the vacuum by maintaining the restraints<br>> then i added ions and water but in the very first minimization i m getting
<br>> the following error<br><br>If you want to keep your credibility, when people have already made a<br>suggestion about how to solve your problem, such as I did here<br><a href="http://www.gromacs.org/pipermail/gmx-users/2007-June/028301.html">
http://www.gromacs.org/pipermail/gmx-users/2007-June/028301.html</a>, when you<br>post the same problem, you should say what happened when you tried their<br>suggestion. They didn't suggest it for their own entertainment.
<br><br>Look at the minimization "trajectory" and see where things are breaking.<br>Have a look at your topology there, read chapter five thoroughly.<br><br>Mark<br><br>_______________________________________________
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