Re: [AMBER] Triply bonded oxygen

From: David A Case <>
Date: Wed, 27 Aug 2014 08:02:51 -0400

On Tue, Aug 26, 2014, Gulsevin,Alican wrote:
> I am working on protonated sugars and their binding energies.
> Therefore, some of my work involve transition state and reactive
> intermediate modelling. However, I've been encountering a problem when
> bond distance is less than 1.9A between a C and an O atom (i.e, 1.8A
> fails to do the resp fitting or AM1-BCC). The error goes similar to
> this:
> For atom[x]:O5, 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 run
> "/usr/local/Amber10/amber10/bin/bondtype -j full -i
> judgebondtype() of antechamber.c properly, exit

You are correct in noting that antechamber won't be of much help here, but
RESP fitting should still work, e.g. through the R.E.D. server, are just by
using resp directly, rather than through the antechamber front-end.

...good luck...dac

AMBER mailing list
Received on Wed Aug 27 2014 - 05:30:03 PDT
Custom Search