AMBER Archive (2004)

Subject: Re: AMBER: prep file

From: James W. Caldwell (jimc_at_stanford.edu)
Date: Mon Jan 05 2004 - 18:01:20 CST

You are missing a blank line after "0 0 2"

jim

On Mon, 2004-01-05 at 15:40, Youyi Peng wrote:
> Hi ALL,
> I made a prepin file for a modified ASP residue. When I loaded into
> leap, I got the message " 0 pairs of atoms within potential bonding
> distance, 0 are not H-H pairs". What does this mean? Any suggestion
> will be highly appreciated.
>
> Youyi Peng
>
> The following is my new prepin file:
>
> 0 0 2
> Modified ASP residue
> AMP.res
> AMP INT 1
> CORR OMIT DU BEG
> 0.00000
> 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
>
> 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
>
> 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000
>
> 4 N N M 3 2 1 1.335 116.600 180.000 -0.52630
>
> 5 H H E 4 3 2 1.010 119.800 0.000 0.29360
>
> 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03810
>
> 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08800
>
> 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.05030
>
> 9 HB2 HC E 8 6 4 1.090 109.500 300.000 -0.01220
>
> 10 HB3 HC E 8 6 4 1.090 109.500 60.000 -0.01220
>
> 11 CG C B 8 6 4 1.527 109.470 180.000 1.10344
>
> 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 -0.83162
>
> 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 -0.84329
>
> 14 C C M 6 4 3 1.522 111.100 180.000 0.51660
>
> 15 O O E 14 6 4 1.229 120.500 0.000 -0.60190
>
> IMPROPER
> -M CA N H
> CA +M C O
> CB OD1 CG OD2
>
> DONE
> STOP
>
>
>
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> 

-- 
James W. Caldwell					650-724-5322
Department of Chemistry
Clark Center, S2.2, Rm S294
Stanford University
Stanford, CA 94305-5447

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