Marcelo Fabricio Masman wrote:
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
you have the wrong order of things in your topology file and you haven't
updated the number of atoms in the gro file (should be 6 fewer)
Generated a cubic box 10.898 x 10.838 x 10.922
double-checking input for internal consistency...
renumbering atomtypes...
Thank you very much.
Marcelo
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
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
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
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
