AMBER Archive (2007)

Subject: Re: AMBER: Torsion terms in xleap

From: Wenyong Tong (wenyong_tong_at_yahoo.com)
Date: Fri Sep 14 2007 - 18:00:20 CDT

"A colleague of mine suggested that I manually add in
the torsion terms into gaff.dat."

Your colleague is right. You can refer some similar
torsion terms in gaff.dat or parm99.dat, and then add
yours.

Have a nice weekend.

Wenyong

--- Lili Peng <lpeng_at_ucsd.edu> wrote:

> 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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