From: Sridhar Vaddadi (Sridhar.Vaddadi_at_utsa.edu)
Date: Thu Sep 24 2009 - 11:34:38 CDT
Dear Community,
I recently started working with NAMD. I generated a pdb file using xyz coordinates and when I visualize in VMD although the structure is looking appropriate, unwanted bonds have been observed. When I tried to generated psf and pdb files from this pdb file, psfgen has generating wrong pdb and psf files with less number of atoms. any suggestions are appreciated.
my pdb file is;
HEADER
ATOM 1 NH1 HSE 1 0.000 0.000 0.000 1.00 0.00
ATOM 2 CT1 HSE 1 0.000 0.000 1.460 1.00 0.00
ATOM 3 C HSE 1 1.404 0.000 2.016 1.00 0.00
ATOM 4 NH1 HSE 1 1.707 1.138 2.655 1.00 0.00
ATOM 5 O HSE 1 2.161 -0.947 1.883 1.00 0.00
ATOM 6 H HSE 1 0.424 -0.765 -0.525 1.00 0.00
ATOM 7 CT2 HSE 1 -0.775 -1.208 1.990 1.00 0.00
ATOM 8 CPH1 HSE 1 -2.235 -1.183 1.656 1.00 0.00
ATOM 9 NR3 HSE 1 -3.110 -0.275 2.213 1.00 0.00
ATOM 10 CPH2 HSE 1 -4.323 -0.490 1.736 1.00 0.00
ATOM 11 NR3 HSE 1 -4.268 -1.501 0.892 1.00 0.00
ATOM 12 CPH1 HSE 1 -2.973 -1.953 0.824 1.00 0.00
ATOM 13 HB HSE 1 -0.501 0.921 1.793 1.00 0.00
ATOM 14 HA HSE 1 -0.330 -2.126 1.579 1.00 0.00
ATOM 15 HA HSE 1 -0.659 -1.254 3.083 1.00 0.00
ATOM 16 H HSE 1 -2.865 0.434 2.873 1.00 0.00
ATOM 17 HR2 HSE 1 -5.226 0.079 1.999 1.00 0.00
ATOM 18 H HSE 1 -5.042 -1.879 0.384 1.00 0.00
ATOM 19 HR1 HSE 1 -2.604 -2.786 0.207 1.00 0.00
ATOM 20 H HSE 1 -0.970 0.017 -0.314 1.00 0.00
ATOM 21 H HSE 1 0.500 0.832 -0.314 1.00 0.00
ATOM 22 CT1 ARG 1 3.020 1.332 3.264 1.00 0.00
ATOM 23 C ARG 1 2.915 1.546 4.755 1.00 0.00
ATOM 24 O ARG 1 3.353 0.721 5.540 1.00 0.00
ATOM 25 OC ARG 1 2.397 2.538 5.240 1.00 0.00
ATOM 26 H ARG 1 0.993 1.864 2.704 1.00 0.00
ATOM 27 CT2 ARG 1 3.737 2.516 2.611 1.00 0.00
ATOM 28 CT2 ARG 1 4.118 2.287 1.158 1.00 0.00
ATOM 29 CT2 ARG 1 4.824 3.499 0.574 1.00 0.00
ATOM 30 NC2 ARG 1 5.197 3.296 -0.821 1.00 0.00
ATOM 31 C ARG 1 5.826 4.200 -1.567 1.00 0.00
ATOM 32 NH2 ARG 1 6.153 5.375 -1.048 1.00 0.00
ATOM 33 NC2 ARG 1 6.125 3.926 -2.829 1.00 0.00
ATOM 34 HB ARG 1 3.606 0.418 3.088 1.00 0.00
ATOM 35 HA ARG 1 3.089 3.403 2.675 1.00 0.00
ATOM 36 HA ARG 1 4.646 2.743 3.187 1.00 0.00
ATOM 37 HA ARG 1 4.773 1.406 1.083 1.00 0.00
ATOM 38 HA ARG 1 3.214 2.067 0.570 1.00 0.00
ATOM 39 HA ARG 1 4.167 4.378 0.653 1.00 0.00
ATOM 40 HA ARG 1 5.726 3.717 1.166 1.00 0.00
ATOM 41 HC ARG 1 4.966 2.420 -1.246 1.00 0.00
ATOM 42 HC ARG 1 5.928 5.582 -0.095 1.00 0.00
END
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