AMBER Archive (2007)

Subject: AMBER: Torsion terms in xleap

From: Lili Peng (lpeng_at_ucsd.edu)
Date: Fri Sep 14 2007 - 17:35:23 CDT

Hi AMBER users,

I have a quick question about preparing a mol2 file in antechamber and
uploading it into xleap. I currently have a mol2 file (see attachment) and
here are the commands I'm running:

1. Generate frcmod file using antechamber: /parmchk -i glu4_linear_PTX.mol2
-f mol2 -o glu4_linear_PTX.frcmod
2. Upload the mol2 file into xleap:
    source leaprc.gaff
    loadamberparams glu4_linear_PTX.frcmod
    loadamberparams gaff.dat
    loadamberparams parm99.dat
    x = loadmol2 glu4_linear_PTX.mol2
    solvatebox x TIP3PBOX 10
    saveamberparm x glu4_linear_PTX.prmtop glu4_linear_PTX.inpcrd

....But then I get the error messages:
1-4: angle 30 35 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 31 34 duplicates bond ('triangular' bond) or angle ('square'
bond)
** No torsion terms for H-C.3-C.3-O.3
** No torsion terms for H-C.3-C.3-H
** No torsion terms for H-C.3-C.3-H
** No torsion terms for O.3-C.3-O.3-H

What is the problem? A colleague of mine suggested that I manually add in
the torsion terms into gaff.dat. How should I go about doing this?

If you have any insight on this problem, I would appreciate it.

Thanks,
Lili


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