molteni at unisi.it
Wed Aug 18 15:56:26 CEST 2004
I'm trying to run gromacs on a peptide containing a "DAL" ( = D-alanine)
residue. I'm using the ffG43a2 force field, which includes this
non-standard residue, but during the (test) simulations the bond between
the amide nitrogen of this residue and the carbonyl C of the preceding one
(that is a "standard" alanine) becomes exceedingly long. I have tried using
a distance restraint between these two atoms, or changing the definitions
or the types of some dihedrals, but nothing seems to work.
As far as i understand, the only difference between ALA and DAL should be
in the definition (maybe the sign?) of one dihedral. And, as far as i see
in the /gromacs/top directory, the only difference is in fact in one of the
impropers, which is "CA-N-C-CB", type=gi_2, in ALA, and "CA-C-N-CB",
type=gi_2 in DAL. The ideal value of this type of dihedral seems to be 35°
(?) So i assume that keeping the same improper type while changing the
order of the atoms results in changing the sign of the improper... (Is this
correct?) that is what we want, since i see in the PDB structure of my
peptide that the dihedrals CA-C-N-CB of the ALA and the DAL residue seem to
have opposite "orientation" (although the value seems to be like 60° rather
than 35°...) Anyway, i don't know if the problem really lies in these
So my questions are:
1) it isn't completely clear to me which of these numbers (in the
dihedral/improper definitions in the ...bon.itp file) is the force
constant, which the ideal angle etc.
2) how can i define a dihedral restraint on a dihedral/improper? I have
tried to do that similarly to distance restraints, but gromacs doesn't seem
to read that. Which are the correct keywords to put in the ...mdp file(s)?
3) more generally..... what can be causing the problem of this long bond
ALA-DAL, and how to avoid it?
many thanks in advance
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