Hi all,
Sorry if this is a stupid question, I'm new to AMBER.
I would like to continue a simulation of an equilibrated structure (100 DME
molecules) which was generated by another MD program. This program uses extra
points as lone pairs located at the oxygen atoms (0.5 Angstroems apart). I
write out the atom positions of the structure to a pdb file. When I run
antechamber to create the prepin it gives the following error:
For atom[2]:O1, the best APS is not zero, bonds involved by this atom are
frozen
For atom[5]:O2, the best APS is not zero, bonds involved by this atom are
frozen
For atom[10]:EP1, the best APS is not zero, bonds involved by this atom are
frozen
For atom[15]:EP2, the best APS is not zero, bonds involved by this atom are
frozen
The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8 (aromatic
double)Error: cannot
How can the lone pairs be incorporated in antechamber? Or are they added later
on? I just wonder because my equilibrated structure already contains exakt
positions of the lone pairs.
Thanks in advance,
Diddo
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Received on Fri Oct 31 2008 - 05:10:37 PDT
