Hi, Jason. Thanks for your reply. I sent this before you replied me
telling me about prepc. I tried prepc and yeah it does not change the
order. Or I will just use mol2. Thanks a lot! Hopefully it work in the
following step.
Joyce
On Tue, Nov 6, 2012 at 5:38 PM, Jason Swails <jason.swails.gmail.com> wrote:
> The format is defined on http://ambermd.org/formats.html
>
> However, is there a reason you insist on using the PREP file instead of the
> MOL2 file? Both work equally well in tleap, and the MOL2 will probably not
> have this problem.
>
> The Amber prep with cartesian coordinates (-prepc instead of -prepi) may
> also not reorder the atoms.
>
> Good luck,
> Jason
>
> On Tue, Nov 6, 2012 at 5:14 PM, Yulin Huang <yulinhuang2007.gmail.com
> >wrote:
>
> > Dear Amber users:
> > I have to map one prep file to another prep file with the same
> > atom order. But I am not
> > clear about the meaning of each column of the prep file. Could anybody
> > explain to me?
> > 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> > 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> > 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
> > 4 C26 ca M 3 2 1 1.540 111.208 180.000
> > -0.101200
> > 5 H24 ha E 4 3 2 1.080 76.455 -25.735
> > 0.108400
> > 6 C27 ca S 4 3 2 1.394 65.190 107.332
> > -0.121500
> > 7 H25 ha E 6 4 3 1.080 118.796 -53.517
> > 0.113700
> > 8 C25 ca M 4 3 2 1.385 131.007 -144.303
> > -0.097000
> > 9 H23 ha E 8 4 3 1.080 120.015 97.374
> > 0.102400
> >
> >
> ...................................................................................................
> >
> > 3rd column: atom types
> > 4th column: tree symbol
> > last column: atom charge
> >
> > What are columns 5th ~ 7th? Is column 8th bond length? 9th angles? 10th
> > dihedrals?
> > If I want to map one file to another, I have to make the columns 5th ~
> 7th
> > the same as the reference?
> >
> > Many thanks in advance.
> >
> >
> >
> > --
> > Yulin "Joyce" Huang
> > Ph.D Candidate
> > Computational Chemistry (CADD)
> > Advisor: Dr. Robert C. Rizzo
> > State University of New York at Stony Brook
> > Stony Brook NY,11790
> > Office: (631)632-8519
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Yulin "Joyce" Huang
Ph.D Candidate
Computational Chemistry (CADD)
Advisor: Dr. Robert C. Rizzo
State University of New York at Stony Brook
Stony Brook NY,11790
Office: (631)632-8519
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 06 2012 - 15:00:03 PST
