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?
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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