AMBER Archive (2007)

Subject: Re: AMBER: pdb flie format

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Sun Jun 03 2007 - 12:57:02 CDT

Reread and export it by MolMol or Pymol.

Best regards.

Fenghui Fan

--- Mr Defang Ouyang <s4131130_at_student.uq.edu.au>
wrote:

> > > 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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