AMBER Archive (2008)

Subject: AMBER: Lone pairs in antechamber

From: Diddo Diddens (d.diddens_at_uni-muenster.de)
Date: Thu Oct 30 2008 - 08:25:35 CDT

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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