[gmx-users] Hi all!

Marcelo Fabricio Masman mmasman at gmail.com
Sun Mar 5 19:20:19 CET 2006

Hi all!!!
I am using the programme grompp (double precision) and the programme genion
to make  "neutral" .top and .tpr files. But after change the quantity of H2O
molecules and add the line with the necessary Na+ ions I am still
having WARNING and the charge is STILL  negative. What happend? What am
I doing wrong? Should I do something else?
Here are the WARNING banners:

Generated 243951 of the 243951 1-4 parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
Excluding 2 bonded neighbours for SOL 41338
WARNING 1 [file "Ab-1.top", line 5860]:
  Too few parameters on line (source file toppush.c, line 1096)
Excluding 2 bonded neighbours for 3 Na+
WARNING 2 [file "Ab-1.top", line 5860]:
  System has non-zero total charge: -3.000000e+00

processing coordinates...
WARNING 3 [file "Ab-1.top", line 5860]:
  Bad box in file Ab-1_n.gro
Generated a cubic box   10.898 x   10.838 x   10.922
double-checking input for internal consistency...
renumbering atomtypes...

Thank you very much.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060305/c2db0dbd/attachment.html>

More information about the gromacs.org_gmx-users mailing list