Dear all :
There is a meatal ion in my protein system.It formed tetrahedron with four residues in the chain.I have got the parameters by using Gaussian and Antechamber.In order to create the residues lib file ,I made the copies of histidine residue in the amino94.lib,and only changed the charges and named it new name HIM .But when I load the HiM.lib file ,the Leap still cannot recognized it.Could someone tell me the reason?Is there other methods if I want to modify one of the residues in the main chain?Thank you very much!
my him.lib
!entry.HIM.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"N" "N" 0 1 131072 1 7 -0.415700
"H" "H" 0 1 131072 2 1 0.271900
"CA" "CT" 0 1 131072 3 6 0.018800
"HA" "H1" 0 1 131072 4 1 0.088100
"CB" "CT" 0 1 131072 5 6 -0.046200
"HB2" "HC" 0 1 131072 6 1 0.040200
"HB3" "HC" 0 1 131072 7 1 0.040200
"CG" "CC" 0 1 131072 8 6 -0.026600
"ND1" "NA" 0 1 131072 9 7 -0.381100
"HD1" "H" 0 1 131072 10 1 0.364900
"CE1" "CR" 0 1 131072 11 6 0.205700
"HE1" "H5" 0 1 131072 12 1 0.139200
"NE2" "NB" 0 1 131072 13 7 -0.572700
"CD2" "CV" 0 1 131072 14 6 0.129200
"HD2" "H4" 0 1 131072 15 1 0.114700
"C" "C" 0 1 131072 16 6 0.597300
"O" "O" 0 1 131072 17 8 -0.567900
!entry.HIM.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
"N" "N" 0 -1 0.0
"H" "H" 0 -1 0.0
"CA" "CT" 0 -1 0.0
"HA" "H1" 0 -1 0.0
"CB" "CT" 0 -1 0.0
"HB2" "HC" 0 -1 0.0
"HB3" "HC" 0 -1 0.0
"CG" "CC" 0 -1 0.0
"ND1" "NA" 0 -1 0.0
"HD1" "H" 0 -1 0.0
"CE1" "CR" 0 -1 0.0
"HE1" "H5" 0 -1 0.0
"NE2" "NB" 0 -1 0.0
"CD2" "CV" 0 -1 0.0
"HD2" "H4" 0 -1 0.0
"C" "C" 0 -1 0.0
"O" "O" 0 -1 0.0
!entry.HID.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.HID.unit.childsequence single int
2
!entry.HIM.unit.connect array int
1
16
!entry.HIM.unit.connectivity table int atom1x int atom2x int flags
1 2 1
1 3 1
3 4 1
3 5 1
3 16 1
5 6 1
5 7 1
5 8 1
8 9 1
8 14 1
9 10 1
9 11 1
11 12 1
11 13 1
13 14 1
14 15 1
16 17 1
!entry.HIm.unit.hierarchy table str abovetype int abovex str belowtype int belowx
"U" 0 "R" 1
"R" 1 "A" 1
"R" 1 "A" 2
"R" 1 "A" 3
"R" 1 "A" 4
"R" 1 "A" 5
"R" 1 "A" 6
"R" 1 "A" 7
"R" 1 "A" 8
"R" 1 "A" 9
"R" 1 "A" 10
"R" 1 "A" 11
"R" 1 "A" 12
"R" 1 "A" 13
"R" 1 "A" 14
"R" 1 "A" 15
"R" 1 "A" 16
"R" 1 "A" 17
!entry.HIM.unit.name single str
"HIM"
!entry.HIM.unit.positions table dbl x dbl y dbl z
3.325770 1.547909 -1.607257E-06
3.909407 0.723611 -2.739904E-06
3.970048 2.845795 -1.312144E-07
3.671663 3.400129 -0.889820
3.576965 3.653838 1.232143
2.496995 3.801075 1.241379
3.877484 3.115795 2.131197
4.200813 5.026064 1.321087
3.942782 5.885086 2.382972
3.339725 5.691913 3.169805
4.624274 6.997642 2.182500
4.563048 7.811875 2.904563
5.294011 6.891451 1.061663
5.058974 5.678868 0.492453
5.537741 5.417846 -0.451343
5.485541 2.705207 -4.398851E-06
6.008824 1.593175 -8.449829E-06
!entry.HIM.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
1 16 0 0 0 0
!entry.HIM.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
"HIM" 1 18 1 "p" 0
!entry.HIM.unit.residuesPdbSequenceNumber array int
0
!entry.HIM.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
!entry.HIM.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
the out :
Creating new UNIT for residue: HIM sequence: 348
Created a new atom named: N within residue: .R<HIM 348>
Created a new atom named: CA within residue: .R<HIM 348>
........
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Received on Mon May 24 2010 - 19:30:03 PDT
