AMBER Archive (2007)

Subject: Re: AMBER: Prepin error (?) in xleap

From: Lili Peng (lilipeng_at_gmail.com)
Date: Fri Aug 24 2007 - 14:26:17 CDT

FYI, I'd like to attach my glu3.mol2 and glu3.ac files. Note: I already
converted the mol2 to ac using: "bondtype -i glu3.mol2 -o glu3.ac -f mol2
-j part" (if I use full I get "bond types are assigned for a valence state
81 with penalty of 4".)

On 8/24/07, Lili Peng <lilipeng_at_gmail.com> wrote:
>
> I created it using prepgen in antechamber:
>
> "prepgen -i glu3.ac -o glu3.prepin -f int -rn GLU3 -rf GLU3.res"
>
> Then I bring up xleap and try to upload the prepin using "loadamberprep
> glu3.prepin"
>
> Something is wrong with the specification of the GLU3 residue too. I
> tried "list" and "check GLU3" and GLU3 didn't show up.
>
> Any ideas what could be wrong?
>
> thanks,
> Lili
>
>
>
>
> On 8/23/07, David A. Case <case_at_scripps.edu> wrote:
> >
> > On Thu, Aug 23, 2007, Lili Peng wrote:
> > >
> > > I'm running into what I think is an error message in xleap when I try
> > to
> > > load my prepin file.
> > >
> > > "this is a remark line atom OE1 type O.co2 : type must be 1 or 2
> > characters"
> > >
> > > What does this mean? Is there something wrong with my prepin file?
> >
> > Probably. How did you create the prepin file? Did you look at it to
> > see
> > if there is an atom called "OE1" with a type " O.co2"? As the message
> > says,
> > Amber and gaff atom types are at most two characters long.
> >
> > ....dac
> >
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>
>


  • application/octet-stream attachment: glu3.mol2

  • application/octet-stream attachment: glu3.ac
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