AMBER: generating parmfile containing topology and parameter information

From: Nitin Bhardwaj <nbhard2.uic.edu>
Date: Mon, 22 Nov 2004 15:29:00 -0600 (CST)

hi all,
   I am trying to generate a parm file for my system which is composed of
a lipid (PIP2), POPC (another lipid) and a protein. I have the pdb files
for all the three molecules. Given below is a copy of my .res file for
residue "INT" in the lipid PIP2.

1) How can I create the parm file containing the topology and parameter
information for PIP2?

2) I have the pdb file only for the lipid "POPC" and I have the other
informattion (parameters and topology) in 'charmm' format. Can I change
the charmm file into an appropriate (properly scaled) 'amber' file format?
Is there an amber topology and parameter file for this lipid 'POPC' or any
other lipid?


I am a complete novice in this regard so I would be very thankful if the
reply could be a detailed one.

thanks,
Nitin





######## .res file for "INT" (a res in PIP2) ###########
INO INT 43 44 80 106 68 228
M OS O01 M CT C02 E HC H03 E HC H04 M CT C05 E HC H06 3
CT
C07 E HC H08 E HC H09 S OS O10 3 P P11 E O2 O12 E O2
O13 S
OS O14 B CT C15 E HC H16 3 CT C17 E HC H18 S OH O19 E HO
H20
3 CT C21 E HC H22 S OH O23 E HO H24 3 CT C25 E HC H26 S
OS
O27 3 P P28 E O2 O29 E O2 O30 E O2 O31 3 CT C32 E HC
H33 S
OS O34 3 P P35 E O2 O36 E O2 O37 E O2 O38 B CT C39 E HC
H40
S OH O41 E HO H42 M OS O43
   1 2 2 3 2 4 2 5 5 6 5 7 5 43 7 8 7 9
7 10
  10 11 11 12 11 13 11 14 14 15 15 16 15 17 15 39 17 18
17 19
  17 21 19 20 21 22 21 23 21 25 23 24 25 26 25 27 25 32
27 28
  28 29 28 30 28 31 32 33 32 34 32 39 34 35 35 36 35 37
35 38
  39 40 39 41 41 42 -50 -50
   1 2 3 1 2 4 1 2 5 2 5 6 2 5 7 2 5 43
3 2
   4 3 2 5 4 2 5 5 7 8 5 7 9 5 7 10 6 5
7 6
   5 43 7 10 11 7 5 43 8 7 9 8 7 10 9 7 10 10
11 12
  10 11 13 10 11 14 11 14 15 12 11 13 12 11 14 13 11 14
14 15
  16 14 15 17 14 15 39 15 17 18 15 17 19 15 17 21 15 39
32 15
  39 40 15 39 41 16 15 17 16 15 39 17 19 20 17 21 22 17
21 23
  17 21 25 17 15 39 18 17 19 18 17 21 19 17 21 21 23 24
21 25
  26 21 25 27 21 25 32 22 21 23 22 21 25 23 21 25 25 27
28 25
  32 33 25 32 34 25 32 39 26 25 27 26 25 32 27 28 29 27
28 30
  27 28 31 27 25 32 29 28 30 29 28 31 30 28 31 32 34 35
32 39
  40 32 39 41 33 32 34 33 32 39 34 35 36 34 35 37 34 35
38 34
  32 39 36 35 37 36 35 38 37 35 38 39 41 42 40 39 41 -50
-50 -50
   1 2 5 6 1 2 5 7 1 2 5 43 2 5 7 8 2 5
7 9
   2 5 7 10 3 2 5 6 3 2 5 7 3 2 5 43 4 2
5 6
   4 2 5 7 4 2 5 43 5 7 10 11 6 5 7 8 6 5
7 9
   6 5 7 10 7 10 11 12 7 10 11 13 7 10 11 14 8 7
10 11
   8 7 5 43 9 7 10 11 9 7 5 43 10 11 14 15 10 7
5 43
  11 14 15 16 11 14 15 17 11 14 15 39 12 11 14 15 13 11
14 15
  14 15 17 18 14 15 17 19 14 15 17 21 14 15 39 32 14 15
39 40
  14 15 39 41 15 17 19 20 15 17 21 22 15 17 21 23 15 39
32 25
  15 17 -21 25 15 39 32 33 15 39 32 34 15 39 41 42 16 15
17 18
  16 15 17 19 16 15 17 21 16 15 39 32 16 15 39 40 16 15
39 41
  17 21 23 24 17 21 25 26 17 21 25 27 17 15 39 32 17 21
-25 32
  17 15 39 40 17 15 39 41 18 17 19 20 18 17 21 22 18 17
21 23
  18 17 21 25 18 17 15 39 19 17 21 22 19 17 21 23 19 17
21 25
  19 17 15 39 20 19 17 21 21 25 27 28 21 25 32 33 21 25
32 34
  21 17 15 39 21 25 -32 39 22 21 23 24 22 21 25 26 22 21
25 27
  22 21 25 32 23 21 25 26 23 21 25 27 23 21 25 32 24 23
21 25
  25 27 28 29 25 27 28 30 25 27 28 31 25 32 34 35 25 32
39 40
  25 32 39 41 26 25 27 28 26 25 32 33 26 25 32 34 26 25
32 39
  27 25 32 33 27 25 32 34 27 25 32 39 28 27 25 32 32 34
35 36
  32 34 35 37 32 34 35 38 32 39 41 42 33 32 34 35 33 32
39 40
  33 32 39 41 34 32 39 40 34 32 39 41 35 34 32 39 40 39
41 42
 -50 -50 -50 -50
  43 43 3 4 43 6 42 8 9 42 42 12 13 42 42 16 42 18
20 20
  42 22 24 24 42 26 31 31 29 30 31 42 33 38 38 36 37 38
42 40
  42 42 43
   0 1 2 2 2 5 5 7 7 7 10 11 11 11 14 15 15 17
17 19
  17 21 21 23 21 25 25 27 28 28 28 25 32 32 34 35 35 35
32 39
  39 41 5
   0 1 1 2 1 3 0 2 1 4 0 2 1 5 1 6 0 5
1 7
   1 8 0 7 1 9 0 7 1 10 1 11 1 12 0 11 1 13
0 11
   1 14 1 15 1 16 0 15 1 17 1 18 0 17 1 19 1 20
0 17
   1 21 1 22 0 21 1 23 1 24 0 21 1 25 1 26 0 25
1 27
   1 28 1 29 0 28 1 30 0 28 1 31 0 25 1 32 1 33
0 32
   1 34 1 35 1 36 0 35 1 37 0 35 1 38 0 32 1 39
1 40
   0 39 1 41 1 42 0 15 1 39 0 5 1 43 2 0
   7 9 5 4 7 5 8 4 3 6 7 3 2 10 16 8 14 7
6 1
  11 6 5 1 13 6 8 4 2 1 1 10 5 7 4 2 1 1
3 2
   1 1 1
   2 3 4 5 6 7 43 3 4 5 6 7 8 9 10 43 4 5
6 7
  43 5 6 7 43 6 7 8 9 10 11 43 7 8 9 10 43 8
9 10
  11 12 13 14 43 9 10 11 43 10 11 43 11 12 13 14 15 43
12 13
  14 15 16 17 39 13 14 15 14 15 15 16 17 18 19 21 32 39
40 41
  16 17 18 19 20 21 22 23 25 32 33 34 39 40 41 42 17 18
19 21
  32 39 40 41 18 19 20 21 22 23 24 25 26 27 32 39 40 41
19 20
  21 22 23 25 39 20 21 22 23 25 39 21 22 23 24 25 26 27
28 32
  33 34 39 23 24 25 26 27 32 24 25 26 27 32 25 26 27 28
29 30
  31 32 33 34 35 39 40 41 27 28 32 33 34 39 28 29 30 31
32 33
  34 39 29 30 31 32 30 31 31 0 33 34 35 36 37 38 39 40
41 42
  34 35 39 40 41 35 36 37 38 39 40 41 36 37 38 39 37 38
38 0
  40 41 42 41 42 42 0 0
 -0.5689 0.6393 -0.0964 -0.0964 -0.4513 0.1893 0.1345 0.0448 0.0448
-0.5520
  1.5088 -0.9414 -0.9414 -0.4555 -0.0601 0.1481 0.0193 0.1199 -0.7594
0.5251
  0.0234 0.0693 -0.4413 0.3214 0.1581 0.1687 -0.4692 1.3342 -1.0003
-1.0003
 -1.0003 0.1043 0.0901 -0.4601 1.2655 -0.9693 -0.9693 -0.9693 -0.0302
0.1845
 -0.4776 0.3579 0.2588
   1.50000 120.00000 0.00000 1.50000 109.00000 180.00000 1.00000
109.00000
 180.00000 1.00000 109.00000 -60.00000 1.53000 111.10000 60.00000
1.00000
 109.00000 51.10000 1.50000 109.00000 170.20000 1.00000 109.00000
60.00000
   1.00000 109.00000 -60.00000 1.50000 120.00000 180.00000 1.60000
119.04000
  65.40000 1.48000 108.20000-175.00000 1.48000 108.20000 -75.00000
1.50000
 102.60000 75.60000 1.50000 109.00000 72.50000 1.00000 109.50000
49.30000
   1.50000 109.00000 -72.50000 1.00000 109.50000 60.00000 1.41000
109.50000
 -60.00000 0.96000 108.50000 60.00000 1.50000 109.00000 180.00000
1.00000
 109.50000 -60.00000 1.41000 109.50000 180.00000 0.96000 108.50000
60.00000
   1.50000 109.00000 60.00000 1.00000 109.50000 60.00000 1.42500
109.50000
-174.50000 1.50000 120.50000 -57.80000 1.48000 108.20000 60.00000
1.48000
 108.20000 -43.50000 1.61000 108.20000-163.39999 1.50000 109.00000
-60.00000
   1.00000 109.50000 -60.00000 1.42500 109.50000 177.30000 1.50000
120.50000
 178.80000 1.48000 108.20000-162.20000 1.48000 108.20000 -42.40000
1.61000
 108.20000 78.30000 1.50000 109.00000 60.00000 1.00000 109.50000
60.00000
   1.41000 109.50000 180.00000 0.96000 108.50000 61.70000 1.22900
120.50000
 -70.50000
####################### FILE END ###################################
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Received on Mon Nov 22 2004 - 21:53:00 PST
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