AMBER Archive (2004)

Subject: AMBER: .lib file error in tleap

From: anita pachaimuthu (anita_pachaimuthu_at_lycos.com)
Date: Mon Jul 19 2004 - 12:19:19 CDT

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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