Dear Nagara,
Which force field are you using?
On Thu, 11 Aug 2005, nag raj wrote:
> 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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--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
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Received on Thu Aug 11 2005 - 16:53:00 PDT
