[gmx-users] D-alanine

[Elena Molteni]

Dear gmx-users
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 
impropers......

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
Elena   
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