[gmx-users] Dihedral not counted?

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 27 16:21:31 CET 2008

Andrea Muntean wrote:
> Hi all,
> I defined my residues for Polystyrene (first, last and inner monomers), 
> with the coresponding bonds, angles, dihedrals and impropers, including 
> also the conectivities (as + and - atoms of the next or previous 
> residue). Pdb2gmx runs without error or warning, but it counts less 
> dihedrals then I would expect. I did run the same for dimer and trimer. 
> For dimer is ok, for trimer starts to count 1 dihedral less, and for the 
> chain with 80 monomers corespondingly 78 dihedrals less, which means 
> that the error should be in the inner residue. I checked many times, but 
> the dihedral which is missing in the .top file is defined in the .rtp. 
> So I have really no clue what is wrong. I runned pdb2gmx also in debug 
> mode, but the log file seem ok to me.
> Please give me a good idea :o)

Without seeing the .rtp entry and the relevant portion of the resulting .top, 
it's hard to say.  Can you post those pieces of information?


> Thanks in advance.
> Andrea
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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