Ragnarok sdf wrote:
Hello, I was following the steps in Justin Lemkul's tutorial for
insertion of a protein in a lipid bilayer and have come accross a
problem right after using inflategro's script from Tieleman's website.
It says there that I should run an energy minimization and then
continue with the steps of the tutorial. Well, I have used the output
structure from inflategro to run an energy minimisation using
grompp/mdrun using a steepest descent algorithm. The problem is that
when I type the command:
grompp -f em_steep.mdp -c inflatedbilayer.gro -p topol.top -o
inflatedbilayer.tpr
The following errors appear:
ERROR 1 [file topol.top, line 523]:
No default G96Angle types
ERROR 2 [file topol.top, line 794]:
No default Proper Dih. types
So what are on these lines? If you can identify which atoms these correspond
to, you will be able to determine whether or not parameters for this angle and
dihedral actually exist within the force field.
-Justin
It seems that I have made some mistake with the forcefield's parameter
files, but I have tried to do everything all over again and the same
errors occur.
Has anyone had any similar problem?
I would appreciate some help if possible.
Thank you
FabrÃcio Bracht
_______________________________________________
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
--
========================================
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
