sreelakshmi ramesh wrote:
Dear all,
when i run energy minimization i get the following error.
the topology file was created from the starting pdb file using g_x2top
*grompp -f em.mdp -c out.gro -p carbon.top -o o.tpr -maxwarn 3*
In general, the use of -maxwarn is discouraged. If grompp fails, then likely
your simulation would too. Using -maxwarn usually just allows you to bypass
critical errors and wind up with a simulation that goes nowhere.
Atoms in the .top are not numbered consecutively from 1 (rather, atomnr
= 348, while at->nr = 0)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
This is a fairly straightforward error message. Your atoms aren't numbered
starting with 1, and they need to be.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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