Hi Wei-Tse
This atom was most likely added by the "reduce" program used by H++ to
"correct the orientation of ASN etc.". Try deselecting this option on the
parameters screen. Let me know if that doesn't work.
Best
Ramu
On Fri, Feb 14, 2020, 12:17 AM Wei-Tse Hsu <Weitse.Hsu.colorado.edu> wrote:
> 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 Fri Feb 14 2020 - 05:30:03 PST
