[gmx-users] 11-cis retinal topology problem

[Albert]

On 07/06/2013 10:17 PM, Mark Abraham wrote:
> That's a completely different output. I think both your executables
> are broken, somehow. Clean the build and install trees and try again
> :-)
>
> Mark


Hello Mark:

thanks a lot for kind messages. The previous problem was solved by 
Justin's sugguestions. Here is the errors from debug:

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#

NOTE 1 [file topol.top, line 1]:
   Debugging
NOTE 2 [file topol.top, line 2]:
   Debugging
NOTE 3 [file topol.top, line 3]:
   Debugging
......
NOTE 18 [file topol.top, line 18]:
   DebugginG
NOTE 19 [file forcefield.itp, line 1]:
   Debugging
NOTE 20 [file forcefield.itp, line 2]:
   Debugging
....
NOTE 3474 [file ffbonded.itp, line 820]:
   Debugging
NOTE 3475 [file ffbonded.itp, line 821]:
   Debugging
-------------------------------------------------------
Program grompp, VERSION 4.6.3
Source code file:
kernel/topdirs.c, line: 106

Fatal error:
Invalid angle type 0
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

I still don't know where is the problem.

thank yo uvery much
Albert