[gmx-users] 11-cis retinal topology problem

Albert mailmd2011 at gmail.com
Sun Jul 7 09:52:21 CEST 2013

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]:
NOTE 2 [file topol.top, line 2]:
NOTE 3 [file topol.top, line 3]:
NOTE 18 [file topol.top, line 18]:
NOTE 19 [file forcefield.itp, line 1]:
NOTE 20 [file forcefield.itp, line 2]:
NOTE 3474 [file ffbonded.itp, line 820]:
NOTE 3475 [file ffbonded.itp, line 821]:
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

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