[gmx-users] RE: No default Proper Dih. types

escajarro juan-manuel.castillo at mv.uni-kl.de
Thu Jan 17 11:40:57 CET 2013

Thank you Justin, but there is still something I do not understand. Could you
please help me with it?

I believe that with the line

 -CB   CA1 +CB  +CA1  gd_34 

in aminoacids.rtp I am defining the torsion the program is complaining
about. I also tried with a line

 -CH3   CH1 +CH2  +CH1  gd_34 

and I still have the same problem. In fact, CB is of type CH3 (defined in
residue MEE) or type CH2 (defined in residue MEM); CA1 of type CH1 (as
defined in residue NIP). The torsion parameters are defined by the set
gd_34, which can be found at ffbonded.itp:

#define gd_34     0.000       5.92          3
; -CHn,SI-CHn-  1.4

As I see it, the torsion for this set of atoms is properly defined in
aminoacids.rtp, and the parameters of the torsion are properly defined in
ffbonded.itp, so they should be read without problems by grompp. What am I
doing wrong? What must be done to declare this torsion for that set of
atoms? I implemented this molecule before using the all-atom OPLS force
field without problems.

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