AMBER Archive (2007)

Subject: AMBER: Lone Pairs

From: Beale, John (jbeale_at_stlcop.edu)
Date: Mon Feb 12 2007 - 12:52:48 CST

How are lone pairs handled in AMBER 8.0 (specifically in FF03)? I am
trying to input a peptide into LEaP. The structure contains one
methionine. The pdb file that I am loading was saved through SYBYL, and
two lone pairs are present in the pdb file, designated as "LPD". . When
I do a loadPdb in LEaP the program tells me that two lone pairs were
added to the structure. I can see the lone pairs when I do an edit in
LEaP. From this step, LEaP doesn't save the prmtop and prmcrd files. If
I edit the pdb file and remove the two lone pairs the parameters are
generated just fine. Has anyone else experienced this problem? Can
someone tell me how I can set this up, leaving the lone pairs in?

 

Thanks!

 

John Beale

 

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