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
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Received on Tue Nov 06 2012 - 15:00:02 PST
