Dear amber users,
I am trying to assign parameters for
DPPC molecule. While saving, i am getting the
following error.
For atom: .R<DPP 1>.A<N2 1> Could not find type: N3
For atom: .R<DPP 1>.A<C4 2> Could not find type: C3
For atom: .R<DPP 1>.A<C3 3> Could not find type: C3
For atom: .R<DPP 1>.A<C1 4> Could not find type: C3
For atom: .R<DPP 1>.A<C5 5> Could not find type: C2
For atom: .R<DPP 1>.A<C6 6> Could not find type: C2
For atom: .R<DPP 1>.A<O7 7> Could not find type: OS
...... ........ .........
........ ....... ..........
Before loading prep and frcmod files i used the
addatom type command.
addAtomTypes {
{ "C3" "C" "sp3" }
{ "C2" "C" "sp3" }
{ "CH" "C" "sp3" }
{ "C" "C" "sp2" }
{ "OS" "O" "sp3" }
{ "O" "O" "sp2" }
{ "O2" "O" "sp2" }
{ "P" "P" "sp3" }
{ "N3" "N" "sp3" }
In this case also i am getting same problem.
Would you tell me how to solve this pboblem.
Here is pdb, prep files.
PREP-FILE:
0 0 2
This is a remark line
molecule.res
DPP XYZ 0
CHANGE OMIT DU BEG
0.0000
1 DUMM DU M 999.000 999.0
-999.0 .00000
2 DUMM DU M 999.000 -999.0
999.0 .00000
3 DUMM DU M -999.000 999.0
999.0 .00000
4 N2 N3 M -11.075000 8.458000
1.343000 -0.50000
5 C4 C3 E -10.735000 8.819000
-0.107000 0.40000
6 C3 C3 E -10.402000 9.434000
2.275000 0.40000
7 C1 C3 E -12.585000 8.550000
1.495000 0.40000
8 C5 C2 M -10.668000 6.978000
1.637000 0.30000
9 C6 C2 M -9.154000 6.725000
1.768000 0.40000
10 O7 OS M -8.451000 6.756000
0.539000 -0.80000
11 P8 P M -8.982000 5.710000
-0.594000 1.70000
12 O10 O2 E -9.532000 4.516000
0.138000 -0.80000
13 O9 O2 E -9.858000 6.519000
-1.512000 -0.80000
14 O11 OS M -7.581000 5.376000
-1.319000 -0.70000
15 C12 C2 M -6.621000 4.616000
-0.600000 0.40000
16 C13 CH M -6.003000 3.575000
-1.538000 0.30000
17 O14 OS S -7.041000 2.613000
-1.837000 -0.70000
18 C15 C B -6.811000 1.722000
-2.828000 0.70000
19 C17 C2 S -7.957000 0.745000
-2.965000 0.00000
20 C18 C2 S -8.593000 0.386000
-1.621000 0.00000
21 C19 C2 S -9.611000 -0.749000
-1.750000 0.00000
22 C20 C2 S -10.300000 -1.009000
-0.408000 0.00000
23 C21 C2 S -11.390000 -2.080000
-0.483000 0.00000
24 C22 C2 S -10.835000 -3.496000
-0.645000 0.00000
25 C23 C2 S -11.963000 -4.532000
-0.611000 0.00000
26 C24 C2 S -11.414000 -5.957000
-0.661000 0.00000
27 C25 C2 S -12.541000 -6.991000
-0.606000 0.00000
28 C26 C2 S -11.983000 -8.413000
-0.557000 0.00000
29 C27 C2 S -13.100000 -9.456000
-0.487000 0.00000
30 C28 C2 S -12.525000 -10.869000
-0.373000 0.00000
31 C29 C2 S -13.627000 -11.925000
-0.302000 0.00000
32 C30 C2 S -13.035000 -13.329000
-0.163000 0.00000
33 C31 C3 E -14.123000 -14.388000
-0.096000 0.00000
34 O16 O E -5.818000 1.710000
-3.546000 -0.70000
35 C32 C2 M -4.811000 2.884000
-0.861000 0.50000
36 O33 OS M -5.292000 2.056000
0.212000 -0.70000
37 C34 C M -4.337000 1.340000
0.859000 0.80000
38 O36 O E -3.131000 1.479000
0.722000 -0.60000
39 C35 C2 M -4.983000 0.281000
1.716000 0.00000
40 C37 C2 M -5.104000 -1.009000
0.913000 0.00000
41 C38 C2 M -5.902000 -2.079000
1.658000 0.00000
42 C39 C2 M -5.953000 -3.376000
0.848000 0.00000
43 C40 C2 M -6.775000 -4.457000
1.552000 0.00000
44 C41 C2 M -6.739000 -5.768000
0.761000 0.00000
45 C42 C2 M -7.595000 -6.849000
1.422000 0.00000
46 C43 C2 M -7.440000 -8.235000
0.784000 0.00000
47 C44 C2 M -7.825000 -8.278000
-0.695000 0.00000
48 C45 C2 M -7.692000 -9.666000
-1.333000 0.00000
49 C46 C2 M -8.674000 -10.706000
-0.785000 0.00000
50 C47 C2 M -8.019000 -11.700000
0.177000 0.00000
51 C48 C2 M -9.047000 -12.697000
0.717000 0.00000
52 C49 C2 M -8.402000 -13.719000
1.651000 0.00000
53 C50 C3 M -9.428000 -14.708000
2.183000 0.00000
LOOP
IMPROPER
C17 O16 C15 O14
C35 O36 C34 O33
DONE
STOP
Here is the Pdb file:
ATOM 1 N2 DPP 1 -11.075 8.458 1.343
1.00 -1.01
ATOM 2 C5 DPP 1 -10.668 6.978 1.637
1.00 0.50
ATOM 3 C6 DPP 1 -9.154 6.725 1.768
1.00 0.28
ATOM 4 O7 DPP 1 -8.451 6.756 0.539
1.00 -0.55
ATOM 5 P8 DPP 1 -8.982 5.710 -0.594
1.00 1.44
ATOM 6 O11 DPP 1 -7.581 5.376 -1.319
1.00 -0.55
ATOM 7 C12 DPP 1 -6.621 4.616 -0.600
1.00 0.28
ATOM 8 C13 DPP 1 -6.003 3.575 -1.538
1.00 0.28
ATOM 9 C32 DPP 1 -4.811 2.884 -0.861
1.00 0.28
ATOM 10 O33 DPP 1 -5.292 2.056 0.212
1.00 -0.43
ATOM 11 C34 DPP 1 -4.337 1.340 0.859
1.00 0.66
ATOM 12 O36 DPP 1 -3.131 1.479 0.722
1.00 -0.57
ATOM 13 C35 DPP 1 -4.983 0.281 1.716
1.00 0.06
ATOM 14 C37 DPP 1 -5.104 -1.009 0.913
1.00 0.00
ATOM 15 C38 DPP 1 -5.902 -2.079 1.658
1.00 0.00
ATOM 16 C39 DPP 1 -5.953 -3.376 0.848
1.00 0.00
ATOM 17 C40 DPP 1 -6.775 -4.457 1.552
1.00 0.00
ATOM 18 C41 DPP 1 -6.739 -5.768 0.761
1.00 0.00
ATOM 19 C42 DPP 1 -7.595 -6.849 1.422
1.00 0.00
ATOM 20 C43 DPP 1 -7.440 -8.235 0.784
1.00 0.00
ATOM 21 C44 DPP 1 -7.825 -8.278 -0.695
1.00 0.00
ATOM 22 C45 DPP 1 -7.692 -9.666 -1.333
1.00 0.00
ATOM 23 C46 DPP 1 -8.674 -10.706 -0.785
1.00 0.00
ATOM 24 C47 DPP 1 -8.019 -11.700 0.177
1.00 0.00
ATOM 25 C48 DPP 1 -9.047 -12.697 0.717
1.00 0.00
ATOM 26 C49 DPP 1 -8.402 -13.719 1.651
1.00 0.00
ATOM 27 C50 DPP 1 -9.428 -14.708 2.183
1.00 0.00
ATOM 28 O14 DPP 1 -7.041 2.613 -1.837
1.00 -0.43
ATOM 29 C15 DPP 1 -6.811 1.722 -2.828
1.00 0.66
ATOM 30 C17 DPP 1 -7.957 0.745 -2.965
1.00 0.06
ATOM 31 C18 DPP 1 -8.593 0.386 -1.621
1.00 0.00
ATOM 32 C19 DPP 1 -9.611 -0.749 -1.750
1.00 0.00
ATOM 33 C20 DPP 1 -10.300 -1.009 -0.408
1.00 0.00
ATOM 34 C21 DPP 1 -11.390 -2.080 -0.483
1.00 0.00
ATOM 35 C22 DPP 1 -10.835 -3.496 -0.645
1.00 0.00
ATOM 36 C23 DPP 1 -11.963 -4.532 -0.611
1.00 0.00
ATOM 37 C24 DPP 1 -11.414 -5.957 -0.661
1.00 0.00
ATOM 38 C25 DPP 1 -12.541 -6.991 -0.606
1.00 0.00
ATOM 39 C26 DPP 1 -11.983 -8.413 -0.557
1.00 0.00
ATOM 40 C27 DPP 1 -13.100 -9.456 -0.487
1.00 0.00
ATOM 41 C28 DPP 1 -12.525 -10.869 -0.373
1.00 0.00
ATOM 42 C29 DPP 1 -13.627 -11.925 -0.302
1.00 0.00
ATOM 43 C30 DPP 1 -13.035 -13.329 -0.163
1.00 0.00
ATOM 44 C31 DPP 1 -14.123 -14.388 -0.096
1.00 0.00
ATOM 45 O16 DPP 1 -5.818 1.710 -3.546
1.00 -0.57
ATOM 46 O10 DPP 1 -9.532 4.516 0.138
1.00 -0.95
ATOM 47 O9 DPP 1 -9.858 6.519 -1.512
1.00 -0.95
ATOM 48 C4 DPP 1 -10.735 8.819 -0.107
1.00 0.50
ATOM 49 C3 DPP 1 -10.402 9.434 2.275
1.00 0.50
ATOM 50 C1 DPP 1 -12.585 8.550 1.495
1.00 0.50
Thank you
nagaraju
____________________________________________________
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Received on Thu Aug 11 2005 - 15:53:00 PDT
