It would be best to post this message on the gmx-users list. It is a
Gromacs-related error message, and not specific to my tutorial.
It is an oft-encountered error, resulting from incorrect updating of your
topology. InflateGRO *did* remove lipids; check the screen output carefully.
Here's how to tell:
grep POPC system_2.gro | wc -l
14716
POPC molecules contain 52 atoms each, so 14716/52 = 283. InflateGRO has
apparently removed 5 lipids from your original 288.
-Justin
Anirban Ghosh wrote:
Respected Sir,
I am trying to simulate a protein embeded in a POPC bilayer. As directed
by you I have followed your tutorial for this. But when executing the
command grompp for generating the .tpr for EM, I am getting the error:
-------------------------------------------------------------------------------
Fatal error:
number of coordinates in coordinate file (system_2.gro, 18636)
does not match topology (topol.top, 18896)
--------------------------------------------------------------------------------
However while using InflateGRO, no lipid molecules were deleted. I am
attaching the files. Please have a look at them and advice. I could not
upload the files at the Gromacs mail list, so am writing to your
personal id. Please advice.
Regards,
--
Anirban Ghosh
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
