Dear Sir/Madam,
I am Satheesh, new to AMBER. I have used tleap(amber11) for generating
protein ligand complex *.prmtop and *.incrd for MD simulations. I have
errors from ligand atom types from protein ligand complex.
I don’t know how to solve the mentioned problem.
Herewith, I have attached the all my files related to above problem.
Please kindly give your answer.
Thank you,
Satheesh.
*Note: Due to security reasons I could not able attach the library file.
here I pasted the .lib file*
!!index array str
"LIG"
!entry.LIG.unit.atoms table str name str type int typex int resx int
flags int seq int elmnt dbl chg
"C1" "c" 0 1 131072 1 6 0.641100
"C2" "c3" 0 1 131072 2 6 -0.077400
"C3" "c3" 0 1 131072 3 6 -0.072400
"C4" "c3" 0 1 131072 4 6 -0.119700
"C5" "c3" 0 1 131072 5 6 -0.072400
"C6" "c3" 0 1 131072 6 6 -0.077400
"C7" "ca" 0 1 131072 7 6 -0.122000
"C8" "ca" 0 1 131072 8 6 -0.126000
"C9" "c3" 0 1 131072 9 6 -0.063100
"C10" "c3" 0 1 131072 10 6 0.089000
"C11" "ca" 0 1 131072 11 6 -0.097300
"C12" "ca" 0 1 131072 12 6 -0.061300
"C13" "c3" 0 1 131072 13 6 -0.079400
"C14" "c" 0 1 131072 14 6 0.683500
"C15" "c3" 0 1 131072 15 6 -0.015000
"C16" "c3" 0 1 131072 16 6 0.056000
"C17" "c3" 0 1 131072 17 6 0.126000
"C18" "ca" 0 1 131072 18 6 -0.125000
"C19" "ca" 0 1 131072 19 6 -0.130000
"N1" "n" 0 1 131072 20 7 -0.442800
"N2" "n" 0 1 131072 21 7 -0.461800
"O1" "o" 0 1 131072 22 8 -0.558100
"O2" "o" 0 1 131072 23 8 -0.643500
"H22" "hc" 0 1 131072 24 1 0.044450
"H23" "hc" 0 1 131072 25 1 0.044450
"H32" "hc" 0 1 131072 26 1 0.050450
"H33" "hc" 0 1 131072 27 1 0.050450
"H4" "hc" 0 1 131072 28 1 0.080700
"H52" "hc" 0 1 131072 29 1 0.050450
"H53" "hc" 0 1 131072 30 1 0.050450
"H62" "hc" 0 1 131072 31 1 0.044450
"H63" "hc" 0 1 131072 32 1 0.044450
"H7" "ha" 0 1 131072 33 1 0.135000
"H8" "ha" 0 1 131072 34 1 0.136000
"H92" "hc" 0 1 131072 35 1 0.063200
"H93" "hc" 0 1 131072 36 1 0.063200
"H102" "h1" 0 1 131072 37 1 0.069700
"H103" "h1" 0 1 131072 38 1 0.069700
"H132" "hc" 0 1 131072 39 1 0.043200
"H133" "hc" 0 1 131072 40 1 0.043200
"H152" "h1" 0 1 131072 41 1 0.095700
"H153" "h1" 0 1 131072 42 1 0.095700
"H162" "h1" 0 1 131072 43 1 0.072200
"H163" "h1" 0 1 131072 44 1 0.072200
"H17" "h1" 0 1 131072 45 1 0.066700
"H18" "ha" 0 1 131072 46 1 0.129000
"H19" "ha" 0 1 131072 47 1 0.134000
!entry.LIG.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
"C1" "c" 0 -1 0.0
"C2" "c3" 0 -1 0.0
"C3" "c3" 0 -1 0.0
"C4" "c3" 0 -1 0.0
"C5" "c3" 0 -1 0.0
"C6" "c3" 0 -1 0.0
"C7" "ca" 0 -1 0.0
"C8" "ca" 0 -1 0.0
"C9" "c3" 0 -1 0.0
"C10" "c3" 0 -1 0.0
"C11" "ca" 0 -1 0.0
"C12" "ca" 0 -1 0.0
"C13" "c3" 0 -1 0.0
"C14" "c" 0 -1 0.0
"C15" "c3" 0 -1 0.0
"C16" "c3" 0 -1 0.0
"C17" "c3" 0 -1 0.0
"C18" "ca" 0 -1 0.0
"C19" "ca" 0 -1 0.0
"N1" "n" 0 -1 0.0
"N2" "n" 0 -1 0.0
"O1" "o" 0 -1 0.0
"O2" "o" 0 -1 0.0
"H22" "hc" 0 -1 0.0
"H23" "hc" 0 -1 0.0
"H32" "hc" 0 -1 0.0
"H33" "hc" 0 -1 0.0
"H4" "hc" 0 -1 0.0
"H52" "hc" 0 -1 0.0
"H53" "hc" 0 -1 0.0
"H62" "hc" 0 -1 0.0
"H63" "hc" 0 -1 0.0
"H7" "ha" 0 -1 0.0
"H8" "ha" 0 -1 0.0
"H92" "hc" 0 -1 0.0
"H93" "hc" 0 -1 0.0
"H102" "h1" 0 -1 0.0
"H103" "h1" 0 -1 0.0
"H132" "hc" 0 -1 0.0
"H133" "hc" 0 -1 0.0
"H152" "h1" 0 -1 0.0
"H153" "h1" 0 -1 0.0
"H162" "h1" 0 -1 0.0
"H163" "h1" 0 -1 0.0
"H17" "h1" 0 -1 0.0
"H18" "ha" 0 -1 0.0
"H19" "ha" 0 -1 0.0
!entry.LIG.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.LIG.unit.childsequence single int
2
!entry.LIG.unit.connect array int
0
0
!entry.LIG.unit.connectivity table int atom1x int atom2x int flags
1 4 1
1 20 1
1 22 2
2 3 1
2 13 1
2 24 1
2 25 1
3 4 1
3 26 1
3 27 1
4 5 1
4 28 1
5 6 1
5 29 1
5 30 1
6 13 1
6 31 1
6 32 1
7 8 4
7 19 4
7 33 1
8 12 4
8 34 1
9 10 1
9 12 1
9 35 1
9 36 1
10 21 1
10 37 1
10 38 1
11 12 4
11 17 1
11 18 4
13 39 1
13 40 1
14 15 1
14 21 1
14 23 2
15 20 1
15 41 1
15 42 1
16 17 1
16 20 1
16 43 1
16 44 1
17 21 1
17 45 1
18 19 4
18 46 1
19 47 1
!entry.LIG.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
"R" 1 "A" 18
"R" 1 "A" 19
"R" 1 "A" 20
"R" 1 "A" 21
"R" 1 "A" 22
"R" 1 "A" 23
"R" 1 "A" 24
"R" 1 "A" 25
"R" 1 "A" 26
"R" 1 "A" 27
"R" 1 "A" 28
"R" 1 "A" 29
"R" 1 "A" 30
"R" 1 "A" 31
"R" 1 "A" 32
"R" 1 "A" 33
"R" 1 "A" 34
"R" 1 "A" 35
"R" 1 "A" 36
"R" 1 "A" 37
"R" 1 "A" 38
"R" 1 "A" 39
"R" 1 "A" 40
"R" 1 "A" 41
"R" 1 "A" 42
"R" 1 "A" 43
"R" 1 "A" 44
"R" 1 "A" 45
"R" 1 "A" 46
"R" 1 "A" 47
!entry.LIG.unit.name single str
"LIG"
!entry.LIG.unit.positions table dbl x dbl y dbl z
24.388000 -4.215000 28.812000
28.023000 -2.725000 29.122000
26.906000 -3.698000 28.673000
25.501000 -3.213000 29.128000
25.220000 -1.743000 28.726000
26.353000 -0.794000 29.202000
17.695000 -0.637000 28.317000
17.747000 -1.495000 27.247000
18.727000 -3.444000 25.989000
19.485000 -4.696000 26.348000
19.720000 -2.544000 28.113000
18.742000 -2.462000 27.122000
27.737000 -1.268000 28.708000
21.905000 -4.891000 26.248000
23.263000 -4.556000 26.787000
22.210000 -2.909000 28.218000
20.853000 -3.570000 28.071000
19.652000 -1.675000 29.204000
18.662000 -0.727000 29.290000
23.229000 -3.971000 28.098000
20.811000 -4.355000 26.834000
24.618000 -5.354000 29.230000
21.837000 -5.630000 25.271000
28.963000 -3.039000 28.670000
28.118000 -2.772000 30.207000
26.919000 -3.771000 27.586000
27.098000 -4.682000 29.099000
25.555000 -3.195000 30.216000
25.139000 -1.681000 27.641000
24.277000 -1.425000 29.172000
26.163000 0.207000 28.814000
26.356000 -0.760000 30.292000
16.907000 0.098000 28.394000
16.993000 -1.418000 26.477000
19.189000 -2.986000 25.115000
17.695000 -3.704000 25.754000
18.944000 -5.235000 27.126000
19.576000 -5.330000 25.466000
28.505000 -0.623000 29.135000
27.773000 -1.193000 27.621000
23.851000 -5.472000 26.833000
23.750000 -3.859000 26.105000
22.351000 -2.167000 27.432000
22.286000 -2.432000 29.195000
20.720000 -4.254000 28.909000
20.389000 -1.749000 29.990000
18.643000 -0.047000 30.129000
!entry.LIG.unit.residueconnect table int c1x int c2x int c3x int c4x
int c5x int c6x
0 0 0 0 0 0
!entry.LIG.unit.residues table str name int seq int childseq int
startatomx str restype int imagingx
"LIG" 1 48 1 "?" 0
!entry.LIG.unit.residuesPdbSequenceNumber array int
0
!entry.LIG.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.LIG.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
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
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
Satheesh.
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Received on Sun Feb 22 2015 - 20:00:02 PST
