Dear everyone,
I'm new to Amber and I was using H++ trying to generate a pdb and a top
file for a protein-ligand binding complex, where the ligand is a 9-residue
long peptide (residue 107 to 115) that contains a phosphotyrosine (residue
111). However, the following errors occured when H++ used tLEaP to process
the file:
FATAL: Atom .R<NASN 107>.A<OXT 17> does not have a type.
FATAL: Atom .R<PTR 111>.A<HB1 25> does not have a type.
There was indeed an OXT atom in residue 107, which is an N-terminal ASN
residue. The first error can be solved by removing the OXT atom (and let
tLEaP to rebuild that atom according to the residue database). However, the
weird thing was that there was even no HB1 atom in the PTR residue (residue
111), so I don't even know which atom to delete. (And I'm not sure what the
number after the atom name means ... like the 25 in HB1 25.) I've made sure
that the protein (chain A) and the ligand (chain B) were separated by a TER
record and I got exactly the same error even if I only used the peptide
part as the input to H++. For your information, the following is the
content of the peptide pdb:
ATOM 875 N ASN B 107 5.572 0.997 -18.517 1.00186.72
N
ATOM 876 CA ASN B 107 5.549 1.484 -17.120 1.00186.72
C
ATOM 877 CB ASN B 107 5.837 2.996 -17.086 1.00186.72
C
ATOM 878 CG ASN B 107 7.333 3.221 -17.230 1.00186.72
C
ATOM 879 OD1 ASN B 107 7.908 3.024 -18.298 1.00186.72
O
ATOM 880 ND2 ASN B 107 7.980 3.641 -16.111 1.00186.72
N
ATOM 881 C ASN B 107 4.198 1.244 -16.423 1.00186.72
C
ATOM 882 O ASN B 107 3.821 1.817 -15.387 1.00186.72
O
ATOM 883 OXT ASN B 107 4.090 1.741 -17.589 1.00186.72
O
ATOM 884 N PRO B 108 3.367 0.246 -16.757 1.00222.35
N
ATOM 885 CA PRO B 108 2.715 -0.662 -15.867 1.00222.35
C
ATOM 886 CD PRO B 108 2.786 0.019 -18.054 1.00222.35
C
ATOM 887 CB PRO B 108 2.758 -1.963 -16.670 1.00222.35
C
ATOM 888 CG PRO B 108 3.036 -1.494 -18.138 1.00222.35
C
ATOM 889 C PRO B 108 3.607 -0.888 -14.692 1.00222.35
C
ATOM 890 O PRO B 108 4.826 -0.901 -14.845 1.00222.35
O
ATOM 891 N GLY B 109 3.011 -1.071 -13.507 1.00 49.98
N
ATOM 892 CA GLY B 109 3.753 -1.332 -12.317 1.00 49.98
C
ATOM 893 C GLY B 109 2.707 -1.713 -11.331 1.00 49.98
C
ATOM 894 O GLY B 109 1.792 -2.466 -11.662 1.00 49.98
O
ATOM 895 N PHE B 110 2.814 -1.203 -10.093 1.00119.85
N
ATOM 896 CA PHE B 110 1.835 -1.564 -9.123 1.00119.85
C
ATOM 897 CB PHE B 110 2.214 -1.658 -7.628 1.00119.85
C
ATOM 898 CG PHE B 110 3.212 -2.756 -7.482 1.00119.85
C
ATOM 899 CD1 PHE B 110 2.821 -4.080 -7.500 1.00119.85
C
ATOM 900 CD2 PHE B 110 4.545 -2.467 -7.306 1.00119.85
C
ATOM 901 CE1 PHE B 110 3.747 -5.087 -7.363 1.00119.85
C
ATOM 902 CE2 PHE B 110 5.477 -3.472 -7.168 1.00119.85
C
ATOM 903 CZ PHE B 110 5.077 -4.784 -7.198 1.00119.85
C
ATOM 904 C PHE B 110 0.524 -0.911 -9.327 1.00119.85
C
ATOM 905 O PHE B 110 -0.466 -1.340 -8.736 1.00119.85
O
ATOM 906 N PTR B 111 0.387 0.163 -10.210 1.00117.85
N
ATOM 907 CA PTR B 111 -0.751 1.014 -10.657 1.00117.85
C
ATOM 908 C PTR B 111 -0.808 1.076 -12.157 1.00117.85
C
ATOM 909 O PTR B 111 0.234 1.165 -12.823 1.00117.85
O
ATOM 910 CB PTR B 111 -0.589 2.388 -10.102 1.00117.85
C
ATOM 911 CG PTR B 111 -0.736 2.463 -8.612 1.00117.85
C
ATOM 912 CD1 PTR B 111 0.380 2.485 -7.807 1.00117.85
C
ATOM 913 CD2 PTR B 111 -1.989 2.521 -8.002 1.00117.85
C
ATOM 914 CE1 PTR B 111 0.271 2.594 -6.429 1.00117.85
C
ATOM 915 CE2 PTR B 111 -2.091 2.574 -6.614 1.00117.85
C
ATOM 916 CZ PTR B 111 -0.971 2.609 -5.830 1.00117.85
C
ATOM 917 OH PTR B 111 -1.031 2.721 -4.495 1.00117.85
O
ATOM 918 P PTR B 111 -1.472 1.580 -3.421 1.00117.85
P
ATOM 919 O1P PTR B 111 -2.367 0.655 -4.118 1.00117.85
O
ATOM 920 O2P PTR B 111 -2.104 2.406 -2.304 1.00117.85
O
ATOM 921 O3P PTR B 111 -0.150 0.959 -2.989 1.00117.85
O
ATOM 922 N VAL B 112 -1.962 1.169 -12.998 1.00 76.89
N
ATOM 923 CA VAL B 112 -2.407 1.257 -14.340 1.00 76.89
C
ATOM 924 CB VAL B 112 -3.602 0.399 -14.632 1.00 76.89
C
ATOM 925 CG1 VAL B 112 -3.197 -1.075 -14.436 1.00 76.89
C
ATOM 926 CG2 VAL B 112 -4.766 0.861 -13.742 1.00 76.89
C
ATOM 927 C VAL B 112 -2.746 2.665 -14.658 1.00 76.89
C
ATOM 928 O VAL B 112 -3.210 3.426 -13.811 1.00 76.89
O
ATOM 929 N GLU B 113 -2.460 3.068 -15.907 1.00 45.51
N
ATOM 930 CA GLU B 113 -2.816 4.387 -16.297 1.00 45.51
C
ATOM 931 CB GLU B 113 -1.950 4.957 -17.432 1.00 45.51
C
ATOM 932 CG GLU B 113 -0.503 5.223 -17.011 1.00 45.51
C
ATOM 933 CD GLU B 113 0.202 5.858 -18.203 1.00 45.51
C
ATOM 934 OE1 GLU B 113 -0.503 6.194 -19.195 1.00 45.51
O
ATOM 935 OE2 GLU B 113 1.451 6.019 -18.132 1.00 45.51
O
ATOM 936 C GLU B 113 -4.224 4.324 -16.787 1.00 45.51
C
ATOM 937 O GLU B 113 -4.636 3.327 -17.377 1.00 45.51
O
ATOM 938 N ALA B 114 -5.013 5.389 -16.550 1.00 59.88
N
ATOM 939 CA ALA B 114 -6.360 5.360 -17.026 1.00 59.88
C
ATOM 940 CB ALA B 114 -7.429 6.153 -16.239 1.00 59.88
C
ATOM 941 C ALA B 114 -6.385 5.778 -18.458 1.00 59.88
C
ATOM 942 O ALA B 114 -5.336 6.048 -19.045 1.00 59.88
O
ATOM 943 N ASN B 115 -7.584 5.875 -19.039 1.00 26.24
N
ATOM 944 CA ASN B 115 -7.713 6.280 -20.460 1.00 26.24
C
ATOM 945 CB ASN B 115 -9.104 5.909 -21.000 1.00 26.24
C
ATOM 946 CG ASN B 115 -9.237 4.391 -21.024 1.00 26.24
C
ATOM 947 OD1 ASN B 115 -8.261 3.669 -21.221 1.00 26.24
O
ATOM 948 ND2 ASN B 115 -10.486 3.892 -20.818 1.00 26.24
N
ATOM 949 C ASN B 115 -7.571 7.794 -20.530 1.00 26.24
C
ATOM 950 O ASN B 115 -7.466 8.414 -19.438 1.00 26.24
O
ATOM 951 OXT ASN B 115 -7.572 8.350 -21.660 1.00 26.24
O
TER 952 ASN B 115
Could someone please provide some suggestions on this? I really had a hard
time dealing with this issue. Any experience shared would be much
appreciated!
Best,
Wei-Tse
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Received on Thu Feb 13 2020 - 21:30:02 PST
