Hi,<div><br></div><div>I have worked around the problem. I was not including a .itp file. But now I am getting Segmentation Fault:</div><div><br></div><div><div>Excluding 1 bonded neighbours for DSPC 104</div><div>Excluding 1 bonded neighbours for W 1397</div>
<div>Excluding 1 bonded neighbours for NA+ 0</div><div>Excluding 1 bonded neighbours for CL- 4</div><div><br></div><div>Number of fg atoms 410288 </div><div>Number of cg atoms 57296 </div><div>Reading frames from gro file 'Protein in DSPC Bilayer', 57296 atoms.</div>
<div>Reading frame 0 time 0.000 1297343010 </div><div>Segmentation fault</div><div><br></div><div><br></div><div>Why is this happening?</div><div><br></div><div><br></div><div>Thanks,</div><div><br></div><div>Anirban</div>
<div><br></div><br><div class="gmail_quote">On Thu, Feb 10, 2011 at 5:45 PM, Anirban Ghosh <span dir="ltr"><<a href="mailto:reach.anirban.ghosh@gmail.com">reach.anirban.ghosh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi Tsjerk,<div><br></div><div>Thanks for the reply.</div><div>Yes, I had a reference to 'Protein' group in my .mdp file while running the CGMD. Now, after CG run I am trying to convert the CG to FG model using:</div>
<div><br></div><div>g_fg2cg -pfg topol_fg.top -pcg system_cg.top -n 0 -c cg.gro -o fg.gro</div><div><br></div><div>So do I need to supply any other parameter to this command or how to mention this refering of 'Protein' group here.</div>
<div><br></div><div>Thanks,</div><div><br></div><font color="#888888"><div>Anirban</div></font><div><div></div><div class="h5"><div><br></div><div><br></div><div><br><div class="gmail_quote">On Thu, Feb 10, 2011 at 5:28 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Anirban,<br>
<br>
Probably you have a reference to a group 'Protein' in your .mdp file.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div><div></div><div><br>
On Thu, Feb 10, 2011 at 12:01 PM, Anirban Ghosh<br>
<<a href="mailto:reach.anirban.ghosh@gmail.com" target="_blank">reach.anirban.ghosh@gmail.com</a>> wrote:<br>
> Hi,<br>
> I am trying to convert a CG system containing multiple copies of a protein +<br>
> lipid + water + ions to an all-atom system using the special gromacs_reverse<br>
> version command g_fg2cg. However I am getting the error:<br>
> -----------------------------------------------------------------------------------------------<br>
> calling cpp...<br>
> processing topology...<br>
> Generated 4 of the 780 non-bonded parameter combinations<br>
> Cleaning up temporary file grompp9YJMaA<br>
> -------------------------------------------------------<br>
> Program g_fg2cg, VERSION 3.3.1<br>
> Source code file: ../kernel/toppush.c, line: 1293<br>
> Fatal error:<br>
> No such moleculetype Protein<br>
> ---------------------------------------------------------------------------------------------<br>
> I have checked all the include statements and .itp files, but cannot fix the<br>
> issue. Is seems to be very trivial but still exists.<br>
> Any suggestion is welcome.<br>
><br>
> Thanks,<br>
> Anirban<br>
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--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
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