AMBER Archive (2004)

Subject: Re: AMBER: .lib file error in tleap

From: Sébastien Osborne (sosborne_at_science.uottawa.ca)
Date: Mon Jul 19 2004 - 13:15:11 CDT

you need to use the loadoff command to load a .lib file. Not loadamberprep.

Sebastien Osborne
University of Ottawa

anita pachaimuthu wrote:

>Hi,
>Iam trying to use some old files that were run on Amber 5 .When i tried to generate the cordiante and topology files usng tleap this is the error i got
>
>
>
>>>loadAmberPrep NDH.lib
>>>
>>>
>Loading Prep file: ./NDH.lib
>Unexpected EOF: discarding residue (!entry.NDH.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg)
>
>
>Can anybody help me figure out the format of this file and how to convert it to the format specified in the manual?.
>
>
>The NDH.lib file looks like this
>
>!!index array str
> "NDH"
>!entry.NDH.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
> "C6N" "CA" 0 1 131072 1 6 -0.355200
> "H6N" "HC" 0 1 131072 2 1 0.221900
> "C5N" "CA" 0 1 131072 3 6 -0.173000
> "H5N" "HC" 0 1 131072 4 1 0.125700
> "C4N" "CT" 0 1 131072 5 6 0.134800
> "H41" "HC" 0 1 131072 6 1 0.019600
> "H42" "HC" 0 1 131072 7 1 0.019600
> "C3N" "CA" 0 1 131072 8 6 -0.222700
> "C7N" "C" 0 1 131072 9 6 0.828500
> "O7N" "O" 0 1 131072 10 8 -0.609900
> "N7N" "N" 0 1 131072 11 7 -0.993500
> "H71" "H" 0 1 131072 12 1 0.404700
> "H72" "H" 0 1 131072 13 1 0.404700
> "C2N" "CA" 0 1 131072 14 6 -0.184000
> "H2N" "HC" 0 1 131072 15 1 0.142200
> "N1N" "N*" 0 1 131072 16 7 0.229300
> "C8N" "CT" 0 1 131072 17 6 -0.038400
> "H8N" "H2" 0 1 131072 18 1 0.161700
> "C9N" "CT" 0 1 131072 19 6 0.067000
> "H9N" "H1" 0 1 131072 20 1 0.097200
> "O10" "OH" 0 1 131072 21 8 -0.613900
> "HO10" "HO" 0 1 131072 22 1 0.418600
> "C11" "CT" 0 1 131072 23 6 0.202200
> "H11" "H1" 0 1 131072 24 1 0.061500
> "O12" "OH" 0 1 131072 25 8 -0.654100
> "HO12" "HO" 0 1 131072 26 1 0.437600
> "C13" "CT" 0 1 131072 27 6 0.106500
> "H13" "H1" 0 1 131072 28 1 0.117400
> "O14" "OS" 0 1 131072 29 8 -0.354800
> "C15" "CT" 0 1 131072 30 6 0.055800
> "H15" "H1" 0 1 131072 31 1 0.067900
> "H16" "H1" 0 1 131072 32 1 0.067900
> "O16" "OS" 0 1 131072 33 8 -0.566100
> "PN" "P" 0 1 131072 34 15 1.372900
> "O17" "O2" 0 1 131072 35 8 -0.855800
> "O18" "O2" 0 1 131072 36 8 -0.855800
> "O19" "OS" 0 1 131072 37 8 -0.576000
> "PA" "P" 0 1 131072 38 15 1.372900
> "O20" "O2" 0 1 131072 39 8 -0.855800
> "O21" "O2" 0 1 131072 40 8 -0.855800
> "O22" "OS" 0 1 131072 41 8 -0.566100
> "C23" "CT" 0 1 131072 42 6 0.055800
>
>
>Thanx in advance
>Anita
>
>

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