[gmx-users] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Nov 4 03:24:39 CET 2009
Chandan Choudhury wrote:
> Hi everyone !!
>
> I am having a problem using pdb2gmx command. Using the command on my
> input pdb file, it results saying Fatal error: Atom O in residue CCMT 1
> not found in rtp entry with 38 atoms while sorting atoms. I do not have
> only "O" either in input pdb file or in rtp file. and its O and not 0
> (zero).
>
> My part of input files reads as
>
> ATOM 1 N CCMT 1 -2.521 -2.813 2.083 0.00 0.00
> ATOM 2 CA CCMT 1 -2.925 -1.739 1.166 0.00 0.00
> ATOM 3 C CCMT 1 -1.711 -0.842 0.859 0.00 0.00
> ATOM 4 CB CCMT 1 -4.034 -0.895 1.821 0.00 0.00
> ATOM 5 SG CCMT 1 -4.523 0.408 0.710 0.00 0.00
> ATOM 6 SD CCMT 1 -5.981 1.512 1.567 0.00 0.00
> ATOM 7 CE CCMT 1 -7.394 0.480 1.895 0.00 0.00
> ATOM 8 CZ CCMT 1 -6.988 -0.662 2.846 0.00 0.00
> ATOM 9 CH CCMT 1 -7.604 -2.072 2.895 0.00 0.00
> ATOM 10 CH1 CCMT 1 -8.797 -2.090 3.869 0.00 0.00
> ATOM 11 CH2 CCMT 1 -8.096 -2.574 1.525 0.00 0.00
> ATOM 12 CI CCMT 1 -5.986 -1.995 4.476 0.00 0.00
> ATOM 13 CI1 CCMT 1 -4.582 -2.406 4.958 0.00 0.00
> ATOM 14 CI2 CCMT 1 -6.931 -2.001 5.692 0.00 0.00
> ATOM 15 CK CCMT 1 -6.018 -0.615 3.792 0.00 0.00
> ATOM 16 NT1 CCMT 1 -6.486 -2.876 3.411 0.00 0.00
> ATOM 17 OC1 CCMT 1 -0.511 -1.346 0.867 0.00 0.00
> ATOM 18 OC2 CCMT 1 -1.885 0.420 0.592 0.00 0.00
> ATOM 19 OT1 CCMT 1 -6.836 -4.122 3.830 0.00 0.00
> ATOM 20 H CCMT 1 -1.801 -3.362 1.658 0.00 0.00
> ATOM 21 HA CCMT 1 -3.292 -2.165 0.256 0.00 0.00
> ATOM 22 HB1 CCMT 1 -4.878 -1.518 2.033 0.00 0.00
> ATOM 23 HB2 CCMT 1 -3.668 -0.468 2.731 0.00 0.00
> ATOM 24 HE1 CCMT 1 -7.754 0.067 0.976 0.00 0.00
> ATOM 25 HE2 CCMT 1 -8.165 1.065 2.350 0.00 0.00
> ATOM 26 HH11 CCMT 1 -9.175 -3.088 3.952 0.00 0.00
> ATOM 27 HH21 CCMT 1 -8.875 -1.932 1.170 0.00 0.00
> ATOM 28 HH12 CCMT 1 -8.477 -1.749 4.832 0.00 0.00
> ATOM 29 HH22 CCMT 1 -7.283 -2.566 0.829 0.00 0.00
> ATOM 30 HH13 CCMT 1 -9.567 -1.446 3.500 0.00 0.00
> ATOM 31 HH23 CCMT 1 -8.471 -3.571 1.624 0.00 0.00
> ATOM 32 HI11 CCMT 1 -4.241 -1.712 5.697 0.00 0.00
> ATOM 33 HI21 CCMT 1 -6.956 -2.982 6.119 0.00 0.00
> ATOM 34 HI12 CCMT 1 -4.624 -3.387 5.383 0.00 0.00
> ATOM 35 HI22 CCMT 1 -6.577 -1.303 6.422 0.00 0.00
> ATOM 36 HI13 CCMT 1 -3.906 -2.405 4.128 0.00 0.00
> ATOM 37 HI23 CCMT 1 -7.915 -1.722 5.380 0.00 0.00
> ATOM 38 HK CCMT 1 -5.391 0.221 4.019 0.00 0.00
What's next in the input PDB file?
Mark
> and my part of .rtp file is
> [ CCMT ]
> [ atoms ]
> N amber99_34 -0.396165 1
> H amber99_17 0.295187 2
> CA amber99_11 -0.073501 3
> HA amber99_19 0.140510 4
> CB amber99_11 -0.221371 5
> HB1 amber99_19 0.146537 6
> HB2 amber99_19 0.146537 7
> SG amber99_48 -0.285182 8
> SD amber99_68 -0.08 9 ;SM
> CE amber99_69 -0.10 10
> HE1 amber99_70 -0.09 11
> HE2 amber99_70 -0.09 12
> CZ amber99_71 -0.003 13
> CH amber99_73 0.334 14
> CH1 amber99_74 -0.337 15
> HH11 amber99_76 0.090 16
> HH12 amber99_76 0.090 17
> HH13 amber99_76 0.090 18
> CH2 amber99_74 -0.337 19
> HH21 amber99_76 0.090 20
> HH22 amber99_76 0.090 21
> HH23 amber99_76 0.090 22
> NT1 amber99_77 0.220 23
> OT1 amber99_78 -0.438 24
> CI amber99_75 0.329 25
> CI1 amber99_74 -0.337 26
> HI11 amber99_76 0.090 27
> HI12 amber99_76 0.090 28
> HI13 amber99_76 0.090 29
> CI2 amber99_74 -0.337 30
> HI21 amber99_76 0.090 31
> HI22 amber99_76 0.090 32
> HI23 amber99_76 0.090 33
> CK amber99_72 -0.340 34
> HK amber99_79 0.162 35
> C amber99_2 0.643035 36
> OC1 amber99_45 -0.79810 37
> OC2 amber99_45 -0.79810 38
>
> Any help is heartly welcomed.
> Thanks in advance
>
> Chandan
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
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