AMBER Archive (2005)

Subject: AMBER: antechamber -- missing improper torsions

From: David Mobley (dmobley_at_gmail.com)
Date: Wed Sep 28 2005 - 17:35:25 CDT

Dear all,

I'm generating AMBER parameters for a small molecule, flavin mononucleotide
(FMN) with AMBER using antechamber on the pdb file (with all hydrogens), and
antechamber is failing to put some of the required improper torsions for
this molecule in the frcmod file that parmchk generates. Any idea why? Here
are the particulars:

I use "antechamber -i (pdb file) -fi pdb -o (mol2 file) -fo mol2 -c bcc",
then run "parmchk -i (mol2 file) -f mol2 -o frcmod". I'm attaching a copy of
the pdb file, which comes from here:
http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?FUNCTION=record&ENTITY=CHEM_COMP&PRIMARYKEY=1569&PARENTINDEX=-1&APPLICATION=1

I am using the latest version of AMBER and just applied all of the bug fixes
two days ago. The errors I get only show up in my leap.log (leap writes out
the prmtop and crd files without complaining) and are:

** Warning: No sp2 improper torsion term for c-ne-cd-cd
atoms are: C4 N5 C4A C10
** Warning: No sp2 improper torsion term for ne-ca-ca-ca
atoms are: N5 C6 C5A C9A
** Warning: No sp2 improper torsion term for ca-ca-ca-ha
atoms are: C5A C7 C6 H6
** Warning: No sp2 improper torsion term for ca-ca-ca-ha
atoms are: C8 C9A C9 H9
** Warning: No sp2 improper torsion term for ca-ca-ca-nh
atoms are: C5A C9 C9A N10
** Warning: No sp2 improper torsion term for ca-cd-nh-c3
atoms are: C9A C10 N10 C1*
** Warning: No sp2 improper torsion term for nc-cd-cd-nh
atoms are: N1 C4A C10 N10

If I proceed while ignoring this, the molecule in question will begin
minimizing in water OK, then exit with an "address error" after several
hundred steps.

If I look through gaff.dat, I can't find improper torsions for the bonds
it's complaining about, so I add the X -X -X -X entry from gaff.dat to my
frcmod file under improper torsions. Strangely, however, it still seems not
to recognize the improper torsions, as it still gives the same warnings in
the leap.log file.

Note: It isn't just that I don't know how to use antechamber or something.
It's worked fine for a number of other small molecules, but seems to be
having problems only with this particular one, for some reason.

Any ideas?

Thanks!
David


  • chemical/x-pdb attachment: fmn.pdb
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu