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

Justin Lemkul jalemkul at vt.edu
Thu Jan 17 11:45:37 CET 2013

On 1/17/13 5:40 AM, escajarro wrote:
> 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

This won't work, because the .rtp file requires atom names, not types.

> 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.

It doesn't work because you're defining a dihedral across 3 residues, and 
pdb2gmx doesn't have machinery to deal with that.  The atoms in question belong 
to MEA, NIP, MEM, then the next NIP.  pdb2gmx can, at most, connect the previous 
residue (using a - prefix) to the next residue (with + prefix), but there is no 
option to include a residue that is two residues downstream.

Either manually add the gd_34 declaration in the .top or revise the way your 
residues are set up so that you don't have one-atom residues.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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