On Mon, Dec 01, 2014, Aronica, Pietro wrote:
> I'm having problems with LEaP. It has problems loading some perfectly
> fine pdb files, because, I suspect, they have more than 100000 atoms. In
> particular, I think it is misinterpreting the CONECT data of the
> disulphide bridges, trying to link cysteines to water molecules and
> crashing out after having an ATOMS NOT BONDED fatal error.
We need more information than this. There is no particular reason why
leap should fail with systems larger than 100000 atoms. Do the CONECT
records go beyond that limit? PDB files allocate six digits for the atom
number, so generally only have problems with more than a million atoms.
There may well be instances where LEaP messes up parsing of CONECT data.
You will probably have to post a file that illustrates the problem. Be sure
that you have converted CYS residues to CYX.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 01 2014 - 05:00:02 PST
