AMBER Archive (2007)

Subject: AMBER: pdb flie format

From: Mr Defang Ouyang (s4131130_at_student.uq.edu.au)
Date: Sun Jun 03 2007 - 07:53:08 CDT

> > Subject: pdb flie format
> >
> > Hi, all,
> >
> > I get the pdb file from material studio, but it cannot input
> into amber
> > by xleap. Could you tell me how to change the pdb file format
> for amber use.
> >
> > REMARK Materials Studio PDB file
> > REMARK Created: Sat May 26 05:44:05 E. Australia Standard
> Time 2007
> > MODEL 1
> > ATOM 1 P DT1 C 1 2.117 1.648 -0.579 1.00
> > 0.00 P
> > ATOM 2 O1P DT1 C 1 1.901 3.317 -1.322 1.00
> > 0.00 O
> > ATOM 3 O2P DT1 C 1 3.107 0.592 -1.715 1.00
> > 0.00 O
> > ATOM 4 O5* DT1 C 1 3.014 1.806 1.018 1.00
> > 0.00 O
> > ATOM 5 C5* DT1 C 1 2.263 2.721 1.954 1.00
> > 0.00 C
> > ATOM 6 1H5* DT1 C 1 1.226 2.282 2.131 1.00
> > 0.00 H
> > ATOM 7 2H5* DT1 C 1 2.159 3.751 1.478 1.00
> > 0.00 H
> > ATOM 8 C4* DT1 C 1 2.986 2.859 3.310 1.00
> > 0.00 C
> > ATOM 9 H4* DT1 C 1 2.345 3.508 3.995 1.00
> > 0.00 H
> > ATOM 10 O4* DT1 C 1 3.215 1.465 3.858 1.00
> > 0.00 O
> > ATOM 11 C1* DT1 C 1 4.704 1.224 3.715 1.00
> > 0.00 C
> > ATOM 12 H1* DT1 C 1 5.199 1.499 4.704 1.00
> > 0.00 H
> > ATOM 13 N1 DT1 C 1 5.042 -0.193 3.323 1.00
> > 0.00 N
> > ATOM 14 C6 DT1 C 1 4.363 -0.501 2.009 1.00
> > 0.00 C
> > ATOM 15 H6 DT1 C 1 4.713 0.240 1.216 1.00
> > 0.00 H
> > ATOM 16 C5 DT1 C 1 4.727 -1.934 1.582 1.00
> > 0.00 C
> > ATOM 17 C7 DT1 C 1 4.024 -2.268 0.252 1.00
> > 0.00 C
> > ATOM 18 H71 DT1 C 1 4.365 -1.533 -0.550 1.00
> > 0.00 H
> > ATOM 19 H72 DT1 C 1 4.292 -3.330 -0.064 1.00
> > 0.00 H
> > ATOM 20 H73 DT1 C 1 2.896 -2.185 0.389 1.00
> > 0.00 H
> > ATOM 21 C4 DT1 C 1 4.263 -2.918 2.672 1.00
> > 0.00 C
> > ATOM 22 O4 DT1 C 1 4.647 -4.323 2.274 1.00
> > 0.00 O
> > ATOM 23 N3 DT1 C 1 4.921 -2.565 3.985 1.00
> > 0.00 N
> > ATOM 24 H3 DT1 C 1 4.582 -3.273 4.770 1.00
> > 0.00 H
> > ATOM 25 C2 DT1 C 1 4.553 -1.155 4.379 1.00
> > 0.00 C
> > ATOM 26 O2 DT1 C 1 5.201 -0.814 5.699 1.00
> > 0.00 O
> > ATOM 27 C3* DT1 C 1 4.403 3.449 3.171 1.00
> > 0.00 C
> > ATOM 28 H3* DT1 C 1 4.452 4.367 2.497 1.00
> > 0.00 H
> > ATOM 29 C2* DT1 C 1 5.168 2.230 2.647 1.00
> > 0.00 C
> > ATOM 30 1H2* DT1 C 1 4.783 1.932 1.618 1.00
> > 0.00 H
> > ATOM 31 2H2* DT1 C 1 6.299 2.367 2.621 1.00
> > 0.00 H
> > ATOM 32 O3* DT1 C 1 4.944 3.769 4.543 1.00
> > 0.00 O
> > TER
> > ENDMDL
> > MODEL 2
> > ATOM 1 N LYS C 1 8.557 -3.001 0.686 1.00
> > 0.00 N
> > ATOM 2 H2 LYS C 1 7.463 -2.811 0.665 1.00
> > 0.00 H
> > ATOM 3 CA LYS C 1 9.298 -1.686 0.686 1.00
> > 0.00 C
> > ATOM 4 HA LYS C 1 9.034 -1.098 -0.254 1.00
> > 0.00 H
> > ATOM 5 CB LYS C 1 8.904 -0.868 1.930 1.00
> > 0.00 C
> > ATOM 6 HB2 LYS C 1 9.174 -1.451 2.871 1.00
> > 0.00 H
> > ATOM 7 HB3 LYS C 1 7.783 -0.662 1.916 1.00
> > 0.00 H
> > ATOM 8 CG LYS C 1 9.671 0.467 1.912 1.00
> > 0.00 C
> > ATOM 9 HG2 LYS C 1 9.397 1.049 0.971 1.00
> > 0.00 H
> > ATOM 10 HG3 LYS C 1 10.793 0.261 1.919 1.00
> > 0.00 H
> > ATOM 11 CD LYS C 1 9.287 1.289 3.156 1.00
> > 0.00 C
> > ATOM 12 HD2 LYS C 1 9.565 0.709 4.097 1.00
> > 0.00 H
> > ATOM 13 HD3 LYS C 1 8.163 1.483 3.149 1.00
> > 0.00 H
> > ATOM 14 CE LYS C 1 10.037 2.634 3.138 1.00
> > 0.00 C
> > ATOM 15 HE2 LYS C 1 9.756 3.213 2.197 1.00
> > 0.00 H
> > ATOM 16 HE3 LYS C 1 11.161 2.442 3.145 1.00
> > 0.00 H
> > ATOM 17 NZ LYS C 1 9.656 3.438 4.359 1.00
> > 0.00 N
> > ATOM 18 HZ2 LYS C 1 8.561 3.621 4.356 1.00
> > 0.00 H
> > ATOM 19 C LYS C 1 10.815 -1.952 0.722 1.00
> > 0.00 C
> > ATOM 20 O LYS C 1 11.334 -3.301 1.157 1.00
> > 0.00 O
> > ATOM 21 O25 LYS C 1 11.776 -0.910 0.203 1.00
> > 0.00 O
> > ATOM 22 H LYS C 1 11.987 -0.177 1.010 1.00
> > 0.00 H
> > ATOM 23 H LYS C 1 10.194 4.409 4.348 1.00
> > 0.00 H
> > ATOM 24 H LYS C 1 8.817 -3.570 1.602 1.00
> > 0.00 H
> > TER
> > ENDMDL
> >
> > Thanks for your help!
> >
> > Ouyang Defang
> > University of Queensland
>

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