lindahl at stanford.edu
Sat Jun 22 00:04:40 CEST 2002
Nguyen Hoang Phuong wrote:
> Dear All,
> I'm building the pdb file for the NMA molecule by combining two residues
> NAC and ACE. After runing the energy minimization, the distance between
> the two residue becomes very large and it seems to be that the molecule
> is broken. I'm using the OPLS force field. Can anyone give me a
> hint? Thanks very much!
NAC and ACE are capping residues on the C- and N-terminus respectively,
and they aren't really intended for standalone molecules. I have NO idea
if the OPLS protein backbone parameters are suitable for a non-capping
NMA (the NAC capping is sometimes called NMA capping).
In any case, you'll have to put the ACE residue before the NAC in your
topology, since the residues are always parsed from N->C terminus.
You will probably have to check the topology manually too, to make sure
all bonds/angles/dihedrals are there.
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