Dear Dr. Case,
I checked the original pdb file which is 1ema.pdb and it has the following
entries
ATOM 455 N PHE A 64 22.250 29.620 36.583 1.00 10.19
N
ATOM 456 CA PHE A 64 21.895 28.371 35.995 1.00 8.00
C
ATOM 457 C PHE A 64 22.774 27.253 36.518 1.00 25.26
C
ATOM 458 O PHE A 64 22.313 26.147 36.761 1.00 9.64
O
ATOM 459 CB PHE A 64 22.114 28.438 34.513 1.00 6.88
C
ATOM 460 CG PHE A 64 21.233 29.357 33.750 1.00 10.96
C
ATOM 461 CD1 PHE A 64 19.899 29.563 34.106 1.00 14.43
C
ATOM 462 CD2 PHE A 64 21.724 29.954 32.593 1.00 9.15
C
ATOM 463 CE1 PHE A 64 19.077 30.375 33.317 1.00 13.95
C
ATOM 464 CE2 PHE A 64 20.936 30.792 31.805 1.00 14.20
C
ATOM 465 CZ PHE A 64 19.597 30.983 32.171 1.00 16.35
C
HETATM 466 N1 CRO A 66 24.077 27.513 36.610 1.00 11.86
N
HETATM 467 CA1 CRO A 66 25.011 26.478 37.078 1.00 7.34
C
HETATM 468 CB1 CRO A 66 25.931 26.035 35.930 1.00 10.77
C
HETATM 469 CG1 CRO A 66 25.155 25.422 34.796 1.00 16.67
C
HETATM 470 OG1 CRO A 66 26.679 27.129 35.461 1.00 14.22
O
HETATM 471 C1 CRO A 66 25.730 27.106 38.245 1.00 18.38
C
HETATM 472 N2 CRO A 66 26.975 27.732 38.216 1.00 9.21
N
HETATM 473 N3 CRO A 66 25.274 27.124 39.509 1.00 17.10
N
HETATM 474 C2 CRO A 66 26.043 27.875 40.370 1.00 5.46
C
HETATM 475 O2 CRO A 66 26.022 27.962 41.566 1.00 13.20
O
HETATM 476 CA2 CRO A 66 27.197 28.245 39.512 1.00 16.08
C
HETATM 477 CA3 CRO A 66 23.919 26.721 39.842 1.00 10.87
C
HETATM 478 C3 CRO A 66 23.745 25.326 40.360 1.00 19.28
C
HETATM 479 O3 CRO A 66 22.885 25.116 41.193 1.00 15.72
O
HETATM 480 CB2 CRO A 66 28.329 28.822 39.960 1.00 10.75
C
HETATM 481 CG2 CRO A 66 29.437 29.370 39.124 1.00 7.67
C
HETATM 482 CD1 CRO A 66 29.541 29.103 37.742 1.00 11.31
C
HETATM 483 CD2 CRO A 66 30.487 30.110 39.805 1.00 10.79
C
HETATM 484 CE1 CRO A 66 30.707 29.546 37.033 1.00 17.44
C
HETATM 485 CE2 CRO A 66 31.614 30.563 39.085 1.00 10.01
C
HETATM 486 CZ CRO A 66 31.718 30.300 37.721 1.00 9.48
C
HETATM 487 OH CRO A 66 32.894 30.804 36.971 1.00 13.84
O
ATOM 488 N VAL A 68 24.535 24.383 39.849 1.00 14.14
N
ATOM 489 CA VAL A 68 24.396 23.004 40.299 1.00 14.40
C
ATOM 490 C VAL A 68 25.784 22.448 40.725 1.00 13.37
C
ATOM 491 O VAL A 68 26.351 21.531 40.123 1.00 10.97
O
ATOM 492 CB VAL A 68 23.757 22.184 39.195 1.00 13.64
C
ATOM 493 CG1 VAL A 68 22.295 22.590 39.007 1.00 13.44
C
*ATOM 494 CG2 VAL A 68 24.520 22.418 37.918 1.00 12.18
C *
................................
the gpf.pdb created after using pdb4amber has these enteries after adding
hydrogens
ATOM 905 N PHE A 63 22.250 29.620 36.583 1.00 10.19
N
ATOM 906 CA PHE A 63 21.895 28.371 35.995 1.00 8.00
C
ATOM 907 C PHE A 63 22.774 27.253 36.518 1.00 25.26
C
ATOM 908 O PHE A 63 22.313 26.147 36.761 1.00 9.64
O
ATOM 909 CB PHE A 63 22.114 28.438 34.513 1.00 6.88
C
ATOM 910 CG PHE A 63 21.233 29.357 33.750 1.00 10.96
C
ATOM 911 CD1 PHE A 63 19.899 29.563 34.106 1.00 14.43
C
ATOM 912 CD2 PHE A 63 21.724 29.954 32.593 1.00 9.15
C
ATOM 913 CE1 PHE A 63 19.077 30.375 33.317 1.00 13.95
C
ATOM 914 CE2 PHE A 63 20.936 30.792 31.805 1.00 14.20
C
ATOM 915 CZ PHE A 63 19.597 30.983 32.171 1.00 16.35
C
ATOM 916 H PHE A 63 22.667 30.298 35.945 1.00 10.19
H
ATOM 917 HA PHE A 63 20.852 28.175 36.242 1.00 8.00
H
ATOM 918 HB2 PHE A 63 23.148 28.732 34.335 1.00 6.88
H
ATOM 919 HB3 PHE A 63 21.993 27.434 34.105 1.00 6.88
H
ATOM 920 HD1 PHE A 63 19.500 29.094 34.993 1.00 14.43
H
ATOM 921 HD2 PHE A 63 22.745 29.763 32.297 1.00 9.15
H
ATOM 922 HE1 PHE A 63 18.045 30.531 33.592 1.00 13.95
H
ATOM 923 HE2 PHE A 63 21.347 31.281 30.935 1.00 14.20
H
ATOM 924 HZ PHE A 63 18.960 31.607 31.561 1.00 16.35
H
HETATM 925 N1 CRO A 64 24.077 27.513 36.610 1.00 11.86
N
HETATM 926 CA1 CRO A 64 25.011 26.478 37.078 1.00 7.34
C
HETATM 927 CB1 CRO A 64 25.931 26.035 35.930 1.00 10.77
C
HETATM 928 CG1 CRO A 64 25.155 25.422 34.796 1.00 16.67
C
HETATM 929 OG1 CRO A 64 26.679 27.129 35.461 1.00 14.22
O
HETATM 930 C1 CRO A 64 25.730 27.106 38.245 1.00 18.38
C
HETATM 931 N2 CRO A 64 26.975 27.732 38.216 1.00 9.21
N
HETATM 932 N3 CRO A 64 25.274 27.124 39.509 1.00 17.10
N
HETATM 933 C2 CRO A 64 26.043 27.875 40.370 1.00 5.46
C
HETATM 934 O2 CRO A 64 26.022 27.962 41.566 1.00 13.20
O
HETATM 935 CA2 CRO A 64 27.197 28.245 39.512 1.00 16.08
C
HETATM 936 CA3 CRO A 64 23.919 26.721 39.842 1.00 10.87
C
HETATM 937 C3 CRO A 64 23.745 25.326 40.360 1.00 19.28
C
HETATM 938 O3 CRO A 64 22.885 25.116 41.193 1.00 15.72
O
HETATM 939 CB2 CRO A 64 28.329 28.822 39.960 1.00 10.75
C
HETATM 940 CG2 CRO A 64 29.437 29.370 39.124 1.00 7.67
C
HETATM 941 CD1 CRO A 64 29.541 29.103 37.742 1.00 11.31
C
HETATM 942 CD2 CRO A 64 30.487 30.110 39.805 1.00 10.79
C
HETATM 943 CE1 CRO A 64 30.707 29.546 37.033 1.00 17.44
C
HETATM 944 CE2 CRO A 64 31.614 30.563 39.085 1.00 10.01
C
HETATM 945 CZ CRO A 64 31.718 30.300 37.721 1.00 9.48
C
HETATM 946 OH CRO A 64 32.894 30.804 36.971 1.00 13.84
O
HETATM 947 HOG1 CRO A 64 27.053 27.620 36.222 1.00 14.22
H
HETATM 948 HG13 CRO A 64 24.613 24.548 35.157 1.00 16.67
H
HETATM 949 HG12 CRO A 64 24.446 26.151 34.404 1.00 16.67
H
HETATM 950 HG11 CRO A 64 25.842 25.122 34.005 1.00 16.67
H
HETATM 951 HA32 CRO A 64 23.531 27.413 40.589 1.00 10.87
H
HETATM 952 HA31 CRO A 64 23.301 26.834 38.951 1.00 10.87
H
HETATM 953 HOH CRO A 64 32.975 30.317 36.124 1.00 13.84
H
HETATM 954 HE2 CRO A 64 32.401 31.118 39.596 1.00 10.01
H
HETATM 955 HE1 CRO A 64 30.825 29.311 35.975 1.00 17.44
H
HETATM 956 HD2 CRO A 64 30.404 30.315 40.872 1.00 10.79
H
HETATM 957 HD1 CRO A 64 28.747 28.568 37.221 1.00 11.31
H
HETATM 958 HB2 CRO A 64 28.447 28.896 41.041 1.00 10.75
H
HETATM 959 HB1 CRO A 64 26.604 25.273 36.323 1.00 10.77
H
HETATM 960 HA1 CRO A 64 24.524 25.558 37.400 1.00 7.34
H
ATOM 961 N VAL A 65 24.535 24.383 39.849 1.00 14.14
N
ATOM 962 CA VAL A 65 24.396 23.004 40.299 1.00 14.40
C
ATOM 963 C VAL A 65 25.784 22.448 40.725 1.00 13.37
C
ATOM 964 O VAL A 65 26.351 21.531 40.123 1.00 10.97
O
ATOM 965 CB VAL A 65 23.757 22.184 39.195 1.00 13.64
C
ATOM 966 CG1 VAL A 65 22.295 22.590 39.007 1.00 13.44
C
*ATOM 967 CG2 VAL A 65 24.520 22.418 37.918 1.00 12.18
C ATOM 968 H3 VAL A 65 23.599 24.836 39.824 1.00 14.14
H ATOM 969 HA VAL A 65 23.747 22.949 41.173 1.00 14.40
H *
ATOM 970 HB VAL A 65 23.788 21.128 39.462 1.00 13.64
H
ATOM 971 HG11 VAL A 65 21.851 21.992 38.211 1.00 13.44
H
ATOM 972 HG12 VAL A 65 21.749 22.422 39.935 1.00 13.44
H
ATOM 973 HG13 VAL A 65 22.242 23.646 38.741 1.00 13.44
H
ATOM 974 HG21 VAL A 65 24.072 21.834 37.114 1.00 12.18
H
ATOM 975 HG22 VAL A 65 24.484 23.477 37.661 1.00 12.18
H
ATOM 976 HG23 VAL A 65 25.558 22.113 38.053 1.00 12.18
H
.....................................................
the gpf.pdb given in the tutorial is like below after adding hydrogens
ATOM 902 N PHE A 63 22.250 29.620 36.583 1.00 10.19
N
ATOM 903 CA PHE A 63 21.895 28.371 35.995 1.00 8.00
C
ATOM 904 C PHE A 63 22.774 27.253 36.518 1.00 25.26
C
ATOM 905 O PHE A 63 22.313 26.147 36.761 1.00 9.64
O
ATOM 906 CB PHE A 63 22.114 28.438 34.513 1.00 6.88
C
ATOM 907 CG PHE A 63 21.233 29.357 33.750 1.00 10.96
C
ATOM 908 CD1 PHE A 63 19.899 29.563 34.106 1.00 14.43
C
ATOM 909 CD2 PHE A 63 21.724 29.954 32.593 1.00 9.15
C
ATOM 910 CE1 PHE A 63 19.077 30.375 33.317 1.00 13.95
C
ATOM 911 CE2 PHE A 63 20.936 30.792 31.805 1.00 14.20
C
ATOM 912 CZ PHE A 63 19.597 30.983 32.171 1.00 16.35
C
ATOM 913 H PHE A 63 22.667 30.298 35.945 1.00 10.19
H
ATOM 914 HA PHE A 63 20.852 28.175 36.242 1.00 8.00
H
ATOM 915 HB2 PHE A 63 23.148 28.732 34.335 1.00 6.88
H
ATOM 916 HB3 PHE A 63 21.993 27.434 34.105 1.00 6.88
H
ATOM 917 HD1 PHE A 63 19.500 29.094 34.993 1.00 14.43
H
ATOM 918 HD2 PHE A 63 22.745 29.763 32.297 1.00 9.15
H
ATOM 919 HE1 PHE A 63 18.045 30.531 33.592 1.00 13.95
H
ATOM 920 HE2 PHE A 63 21.347 31.281 30.935 1.00 14.20
H
ATOM 921 HZ PHE A 63 18.960 31.607 31.561 1.00 16.35
H
HETATM 922 N1 CRO A 64 24.077 27.513 36.610 1.00 11.86
N
HETATM 923 CA1 CRO A 64 25.011 26.478 37.078 1.00 7.34
C
HETATM 924 CB1 CRO A 64 25.931 26.035 35.930 1.00 10.77
C
HETATM 925 CG1 CRO A 64 25.155 25.422 34.796 1.00 16.67
C
HETATM 926 OG1 CRO A 64 26.679 27.129 35.461 1.00 14.22
O
HETATM 927 C1 CRO A 64 25.730 27.106 38.245 1.00 18.38
C
HETATM 928 N2 CRO A 64 26.975 27.732 38.216 1.00 9.21
N
HETATM 929 N3 CRO A 64 25.274 27.124 39.509 1.00 17.10
N
HETATM 930 C2 CRO A 64 26.043 27.875 40.370 1.00 5.46
C
HETATM 931 O2 CRO A 64 26.022 27.962 41.566 1.00 13.20
O
HETATM 932 CA2 CRO A 64 27.197 28.245 39.512 1.00 16.08
C
HETATM 933 CA3 CRO A 64 23.919 26.721 39.842 1.00 10.87
C
HETATM 934 C3 CRO A 64 23.745 25.326 40.360 1.00 19.28
C
HETATM 935 O3 CRO A 64 22.885 25.116 41.193 1.00 15.72
O
HETATM 936 CB2 CRO A 64 28.329 28.822 39.960 1.00 10.75
C
HETATM 937 CG2 CRO A 64 29.437 29.370 39.124 1.00 7.67
C
HETATM 938 CD1 CRO A 64 29.541 29.103 37.742 1.00 11.31
C
HETATM 939 CD2 CRO A 64 30.487 30.110 39.805 1.00 10.79
C
HETATM 940 CE1 CRO A 64 30.707 29.546 37.033 1.00 17.44
C
HETATM 941 CE2 CRO A 64 31.614 30.563 39.085 1.00 10.01
C
HETATM 942 CZ CRO A 64 31.718 30.300 37.721 1.00 9.48
C
HETATM 943 OH CRO A 64 32.894 30.804 36.971 1.00 13.84
O
HETATM 944 HOG1 CRO A 64 27.053 27.620 36.222 1.00 14.22
H
HETATM 945 HG13 CRO A 64 24.613 24.548 35.157 1.00 16.67
H
HETATM 946 HG12 CRO A 64 24.446 26.151 34.404 1.00 16.67
H
HETATM 947 HG11 CRO A 64 25.842 25.122 34.005 1.00 16.67
H
HETATM 948 HA32 CRO A 64 23.531 27.413 40.589 1.00 10.87
H
HETATM 949 HA31 CRO A 64 23.301 26.834 38.951 1.00 10.87
H
HETATM 950 HOH CRO A 64 32.975 30.317 36.124 1.00 13.84
H
HETATM 951 HE2 CRO A 64 32.401 31.118 39.596 1.00 10.01
H
HETATM 952 HE1 CRO A 64 30.825 29.311 35.975 1.00 17.44
H
HETATM 953 HD2 CRO A 64 30.404 30.315 40.872 1.00 10.79
H
HETATM 954 HD1 CRO A 64 28.747 28.568 37.221 1.00 11.31
H
HETATM 955 HB2 CRO A 64 28.447 28.896 41.041 1.00 10.75
H
HETATM 956 HB1 CRO A 64 26.604 25.273 36.323 1.00 10.77
H
HETATM 957 HA1 CRO A 64 24.524 25.558 37.400 1.00 7.34
H
ATOM 958 N VAL A 65 24.535 24.383 39.849 1.00 14.14
N
ATOM 959 CA VAL A 65 24.396 23.004 40.299 1.00 14.40
C
ATOM 960 C VAL A 65 25.784 22.448 40.725 1.00 13.37
C
ATOM 961 O VAL A 65 26.351 21.531 40.123 1.00 10.97
O
ATOM 962 CB VAL A 65 23.757 22.184 39.195 1.00 13.64
C
ATOM 963 CG1 VAL A 65 22.295 22.590 39.007 1.00 13.44
C
*ATOM 964 CG2 VAL A 65 24.520 22.418 37.918 1.00 12.18
C ATOM 965 HA VAL A 65 23.747 22.949 41.173 1.00 14.40
H *
ATOM 966 HB VAL A 65 23.788 21.128 39.462 1.00 13.64
H
ATOM 967 HG11 VAL A 65 21.851 21.992 38.211 1.00 13.44
H
ATOM 968 HG12 VAL A 65 21.749 22.422 39.935 1.00 13.44
H
ATOM 969 HG13 VAL A 65 22.242 23.646 38.741 1.00 13.44
H
ATOM 970 HG21 VAL A 65 24.072 21.834 37.114 1.00 12.18
H
ATOM 971 HG22 VAL A 65 24.484 23.477 37.661 1.00 12.18
H
ATOM 972 HG23 VAL A 65 25.558 22.113 38.053 1.00 12.18
H
......................................
There is no TER card in the original and I cant find a reason why the
Hydrogen atom should be added. and this was not the only addition. there
were other residues where the hydrogen was added and there was no similar
entry in the tutorial generated file.
My question is if I delete the atom manually, I have to renumber the atoms.
how is it done as I could not find anyone asking this query for me to
follow the command line.
Thank you
Regards
On Mon, Aug 24, 2020 at 9:39 AM David A Case <david.case.rutgers.edu> wrote:
> On Mon, Aug 24, 2020, Ayesha Fatima wrote:
> >
> >FATAL: Atom .R<VAL 65>.A<H3 17> does not have a type.
>
> Somehow the program thinks that your VAL 65 is at the N-terminus of a new
> chain. Look at the PDB file that is the input for this, and see if you can
> figure out what is going on: is there a TER card preceding VAL65, or some
> other clue? If you study the leap.log file carefully, you will probably
> find
> a message that says residue 65 is being assigned to NVAL (an N-terminal
> valine).
>
> We are trying to get people to go through the tutorials, which can easily
> get
> out of date. But see if you can figure out what is going on. Did you do
> anything different from what was described on the web site?
>
> ....regards...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Aug 24 2020 - 09:30:04 PDT
