RE: AMBER: tleap,xleap bond order for triple bonds

From: Ross Walker <ross.rosswalker.co.uk>
Date: Tue, 29 Mar 2005 15:58:51 -0800

Hi Julie,

> I'm having a lot of trouble setting a triple bond in xleap
> and tleap. I do a: bond ABC.1.C3 ABC.1.C4 "#"
> and I either get a syntax error or an illegal bond order message.
> My triple bond is adjacent to single bonds on both sides.

It appears that the use of # is not supported on all architectures. Some
architectures treat it as some kind of comment character and don't pass it
as an option to the bond subroutine.

Try applying the attached bugfix.42 file to $AMBERHOME/src/leap/src/leap and
then recompile leap with

cd $AMBEROME/src/leap
make clean
make

This will replace the -,=,#,: with S,D,T,A for single, double, triple or
aromatic bonds respectively.

All the best
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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Received on Wed Mar 30 2005 - 01:53:01 PST
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