VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Feb 17 2007 - 15:36:45 CST

Hi Mario,
there appears to be some platform-specific weirdness going on with the
plugin. I'll have a look and get back to you. Thanks for pointing this out.
Peter

Mario Valle wrote:
> The save coordinates with format MOL2 produces a strange result file.
> Load the attached PDB file (extracted from PDB 6RSA) and then save
> coordinates as MOL2 format (attached).
> Notice the strange t[SOH] after the atom type, the V and D atoms
> (corrected in VMD) exported as type X. idem for 1H2 and 2H2 hydrogen
> atoms.
> Tested on Windows with 1.8.5
>
> Have a nice weekend!
> mario
>
>
> ------------------------------------------------------------------------
>
> CRYST1 30.300 38.350 53.700 90.00 106.40 90.00 P 1 1
> ATOM 1 O5* UVC X 1 33.514 12.846 5.813 1.00 20.91 6RSA
> ATOM 2 C5* UVC X 1 32.332 13.231 5.108 1.00 19.28 6RSA
> ATOM 3 C4* UVC X 1 31.472 13.945 6.112 1.00 18.91 6RSA
> ATOM 4 O4* UVC X 1 31.432 13.033 7.258 1.00 17.18 6RSA
> ATOM 5 C3* UVC X 1 31.862 15.373 6.590 1.00 18.53 6RSA
> ATOM 6 O3* UVC X 1 31.488 16.498 5.719 1.00 20.00 6RSA
> ATOM 7 C2* UVC X 1 31.041 15.368 7.854 1.00 17.77 6RSA
> ATOM 8 O2* UVC X 1 29.722 15.834 7.639 1.00 19.26 6RSA
> ATOM 9 C1* UVC X 1 30.899 13.890 8.308 1.00 16.41 6RSA
> ATOM 10 N1 UVC X 1 31.969 13.661 9.352 1.00 15.10 6RSA
> ATOM 11 C2 UVC X 1 31.656 13.999 10.612 1.00 13.91 6RSA
> ATOM 12 O2 UVC X 1 30.578 14.391 10.997 1.00 13.09 6RSA
> ATOM 13 N3 UVC X 1 32.670 13.732 11.468 1.00 14.76 6RSA
> ATOM 14 C4 UVC X 1 33.945 13.283 11.176 1.00 15.07 6RSA
> ATOM 15 O4 UVC X 1 34.772 13.201 12.075 1.00 17.08 6RSA
> ATOM 16 C5 UVC X 1 34.175 13.003 9.795 1.00 14.52 6RSA
> ATOM 17 C6 UVC X 1 33.174 13.182 8.937 1.00 13.84 6RSA
> ATOM 18 V UVC X 1 29.854 17.210 6.366 1.00 19.32 6RSA
> ATOM 19 O1V UVC X 1 28.228 17.098 5.741 1.00 18.30 6RSA
> ATOM 20 O2V UVC X 1 30.159 18.258 4.797 1.00 20.33 6RSA
> ATOM 21 O3V UVC X 1 29.927 18.625 7.388 1.00 19.00 6RSA
> ATOM 22 D1 UVC X 1 34.322 13.296 5.377 1.00 21.05 6RSA
> ATOM 23 1H2 UVC X 1 31.942 12.471 4.642 1.00 19.45 6RSA
> ATOM 24 2H2 UVC X 1 32.688 13.883 4.421 1.00 19.31 6RSA
> ATOM 25 H3 UVC X 1 30.529 14.148 5.817 1.00 18.35 6RSA
> ATOM 26 H5 UVC X 1 32.848 15.496 6.319 1.00 19.02 6RSA
> ATOM 27 H7 UVC X 1 31.548 16.016 8.486 1.00 17.96 6RSA
> ATOM 28 H9 UVC X 1 29.987 13.681 8.639 1.00 16.34 6RSA
> ATOM 29 D13 UVC X 1 32.483 13.948 12.465 1.00 14.54 6RSA
> ATOM 30 H16 UVC X 1 35.098 12.662 9.551 1.00 14.60 6RSA
> ATOM 31 H17 UVC X 1 33.322 13.009 7.940 1.00 14.29 6RSA
> END
>