[gmx-users] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 4 12:51:34 CET 2009
Chandan Choudhury wrote:
> My complete input file is
>
> 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
> ATOM 39 N NARG 2 -4.657 -5.920 2.257 0.00 0.00
> ATOM 40 CA NARG 2 -3.476 -5.161 2.694 0.00 0.00
> ATOM 41 C NARG 2 -3.680 -3.668 2.378 0.00 0.00
> ATOM 42 O NARG 2 -4.839 -3.179 2.371 0.00 0.00
> ATOM 43 CB NARG 2 -2.230 -5.679 1.952 0.00 0.00
> ATOM 44 CG NARG 2 -0.992 -4.885 2.410 0.00 0.00
> ATOM 45 CZ NARG 2 2.459 -4.459 1.265 0.00 0.00
> ATOM 46 CD NARG 2 0.254 -5.404 1.668 0.00 0.00
> ATOM 47 NE NARG 2 1.436 -4.648 2.106 0.00 0.00
> ATOM 48 NH1 NARG 2 2.406 -4.958 0.025 0.00 0.00
> ATOM 49 NH2 NARG 2 3.535 -3.771 1.664 0.00 0.00
> ATOM 50 HA NARG 2 -3.341 -5.287 3.748 0.00 0.00
> ATOM 51 HB1 NARG 2 -2.089 -6.716 2.172 0.00 0.00
> ATOM 52 HB2 NARG 2 -2.365 -5.552 0.898 0.00 0.00
> ATOM 53 HG1 NARG 2 -1.132 -3.847 2.190 0.00 0.00
> ATOM 54 HG2 NARG 2 -0.858 -5.011 3.464 0.00 0.00
> ATOM 55 HD1 NARG 2 0.393 -6.442 1.888 0.00 0.00
> ATOM 56 HD2 NARG 2 0.120 -5.278 0.614 0.00 0.00
> ATOM 57 HE NARG 2 1.475 -4.274 3.033 0.00 0.00
> ATOM 58 HH11 NARG 2 1.602 -5.472 -0.274 0.00 0.00
> ATOM 59 HH21 NARG 2 3.574 -3.398 2.591 0.00 0.00
> ATOM 60 HH12 NARG 2 3.171 -4.817 -0.604 0.00 0.00
> ATOM 61 HH22 NARG 2 4.299 -3.631 1.035 0.00 0.00
> ATOM 62 H1 NARG 2 -5.466 -5.584 2.740 0.00 0.00
> ATOM 63 H2 NARG 2 -4.525 -6.890 2.463 0.00 0.00
> ATOM 64 H3 NARG 2 -4.783 -5.802 1.272 0.00 0.00
> END
>
>
Is your goal a dipeptide of NARG-CCMT? If so, think about the order. If CCMT
comes first, pdb2gmx is going to try to make an amide bond between the
carboxylate of CCMT and the amino group of NARG, deleting and replacing whatever
it has to. Does your CCMT .rtp entry define any bonds, or is it just the atom
entries you showed before?
I would suggest putting the amino acids in the proper order (N-terminal first)
and see if that fixes the problem.
-Justin
>
> On Wed, Nov 4, 2009 at 7:54 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
> 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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>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> ------------------------------------------------------------------------
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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