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
On Wed, Nov 4, 2009 at 7:54 AM, Mark Abraham <mark.abra...@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 >> >> >> ------------------------------------------------------------------------ >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Chandan kumar Choudhury NCL, Pune INDIA
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
