[gmx-users] How to avoid generating wrong dihedrals?(Tsjerk)

wuxiao xiaowu759 at hotmail.com
Wed Jul 1 10:42:31 CEST 2009

Dear Tsjerk and other gmx users and developers,

  I use OPLS-AA force field to model a dendrimer PAMAM. And the addition of hydrogens is found correct. The rtp files were written for the core, middle and end repeating units, respectively.  The both repeating units cause the problem. When I delete all those wrong dihedrals in the top file, the grompp and mdrun can run successfully. I check the top file. It seems that other dihedrals are all correct. What to happen to this? Could you give me further information? Any reply would be thanked very much.



Chaofu Wu


>Hi Chaofu Wu,
>Indeed it seems improper to have a dihedral with C-N-H-H. So it's an
>improper dihedral! :p
>The problem might arise from the addition of hydrogens. Could you give
>more information? Which force field did you use?

>what residue was causing the problem? Can you reproduce the problem starting only with
>that residue (and then paste it, so that one of us might reproduce

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