cbaakman
commented
4 years ago The column numbers are wrong. Atom number, atom name, etc. should always be on fixed columns.
Please check the PDB format description: https://zhanglab.ccmb.med.umich.edu/SSIPe/pdb_atom_format.html#ATOM
this is my pdb format： ATOM 1 N ASP A 1 63.210 21.960 131.820 1.00 0.00 N ATOM 2 HT1 ASP A 1 64.020 22.090 132.450 1.00 0.00 H ATOM 3 HT2 ASP A 1 63.160 20.960 131.520 1.00 0.00 H ATOM 4 HT3 ASP A 1 62.360 22.160 132.380 1.00 0.00 H ATOM 5 CA ASP A 1 63.150 22.770 130.580 1.00 0.00 C ATOM 6 HA ASP A 1 64.130 22.970 130.160 1.00 0.00 H ATOM 7 CB ASP A 1 62.410 21.990 129.410 1.00 0.00 C ATOM 8 HB1 ASP A 1 62.120 22.760 128.660 1.00 0.00 H ATOM 9 HB2 ASP A 1 61.520 21.520 129.870 1.00 0.00 H ATOM 10 CG ASP A 1 63.320 21.030 128.700 1.00 0.00 C ATOM 11 OD1 ASP A 1 64.520 20.810 129.070 1.00 0.00 O ATOM 12 OD2 ASP A 1 62.850 20.540 127.630 1.00 0.00 O ATOM 13 C ASP A 1 62.590 24.130 130.890 1.00 0.00 C ATOM 14 O ASP A 1 63.230 25.160 131.110 1.00 0.00 O I use [gmx trjconv -dump] to generate this pdb file . What are the problems of my pdb file?