VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 16 2007 - 18:39:17 CDT

Hi,
  Can you try using VMD 1.8.6? The mol2 plugin was updated
a little while back to correct some issues which should hopefully
address the problem you're experiencing as well. Let me know if
that solves the problem or not.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Apr 16, 2007 at 08:32:28PM -0300, Cesar Luis Avila wrote:
> Dear all,
> I am using vmd 1.8.5 for linux (debian 32 bits). I loaded a NAD molecule
> from pdb file and then I tried to save it as mol2 using
> $sel writemol2 nad.mol2
> The problem I am facing is that some strange characters appear on the
> file, preventing it to get read from other programs. VMD apparently has
> no problem opening it.
> Regards
> Cesar Avila
>
> @<TRIPOS>MOLECULE
> generated by VMD
> 44 48 1 0 0
> SMALL
> NO_CHARGES
> ****
> Energy = 0
>
> @<TRIPOS>ATOM
> 1 AP -8.2880 -20.3740 8.8430 X. ???R??r?? 2336 NAD 0.000000
> 2 AO1 -9.3500 -20.0920 7.8510 X. ???R??r?? 2336 NAD 0.000000
> 3 AO2 -7.9350 -19.7360 10.1450 X. ???R??r?? 2336 NAD 0.000000
> 4 AO5* -7.8290 -21.9190 8.7230 X. ???R??r?? 2336 NAD 0.000000
> 5 AC5* -8.1520 -22.7850 7.5740 X. ???R??r?? 2336 NAD 0.000000
> 6 AC4* -6.8530 -23.1850 6.8800 X. ???R??r?? 2336 NAD 0.000000
> 7 AO4* -7.2570 -24.0680 5.7590 X. ???R??r?? 2336 NAD 0.000000
> 8 AC3* -6.0380 -22.0320 6.1740 X. ???R??r?? 2336 NAD 0.000000
> 9 AO3* -4.6970 -21.9380 6.7400 X. ???R??r?? 2336 NAD 0.000000
> 10 AC2* -6.0400 -22.3590 4.6830 X. ???R??r?? 2336 NAD 0.000000
> 11 AO2* -4.9400 -21.9710 3.9220 X. ???R??r?? 2336 NAD 0.000000
> 12 AC1* -6.3260 -23.8770 4.7130 X. ???R??r?? 2336 NAD 0.000000
> 13 AN9 -6.9850 -24.3510 3.4920 X. ???R??r?? 2336 NAD 0.000000
> 14 AC8 -7.9130 -23.7720 2.6210 X. ???R??r?? 2336 NAD 0.000000
> 15 AN7 -8.2650 -24.5570 1.6140 X. ???R??r?? 2336 NAD 0.000000
> 16 AC5 -7.5920 -25.7140 1.7520 X. ???R??r?? 2336 NAD 0.000000
> 17 AC6 -7.5580 -26.9670 0.9630 X. ???R??r?? 2336 NAD 0.000000
> 18 AN6 -8.2790 -27.1420 -0.1320 X. ???R??r?? 2336 NAD 0.000000
> 19 AN1 -6.7050 -27.9480 1.4650 X. ???R??r?? 2336 NAD 0.000000
> 20 AC2 -5.9430 -27.8340 2.5740 X. ???R??r?? 2336 NAD 0.000000
> 21 AN3 -5.9380 -26.6680 3.3600 X. ???R??r?? 2336 NAD 0.000000
> 22 AC4 -6.7780 -25.6270 2.9160 X. ???R??r?? 2336 NAD 0.000000
> 23 O3 -9.5240 -20.9530 9.7290 O.2 ???R??r?? 2336 NAD 0.000000
> 24 NP -9.7760 -21.4120 11.3090 N.3 ???R??r?? 2336 NAD 0.000000
> 25 NO1 -10.1510 -20.2200 12.0970 N.3 ???R??r?? 2336 NAD 0.000000
> 26 NO2 -8.5710 -22.2120 11.7100 N.3 ???R??r?? 2336 NAD 0.000000
> 27 NO5* -11.1120 -22.3300 11.1420 N.3 ???R??r?? 2336 NAD 0.000000
> 28 NC5* -11.0620 -23.6020 10.4070 N.3 ???R??r?? 2336 NAD 0.000000
> 29 NC4* -12.1620 -24.5040 10.8530 N.3 ???R??r?? 2336 NAD 0.000000
> 30 NO4* -12.2250 -24.5220 12.3470 N.3 ???R??r?? 2336 NAD 0.000000
> 31 NC3* -13.6110 -24.0670 10.3990 N.3 ???R??r?? 2336 NAD 0.000000
> 32 NO3* -14.3580 -25.2030 9.9090 N.3 ???R??r?? 2336 NAD 0.000000
> 33 NC2* -14.2560 -23.4960 11.6770 N.am ???R??r?? 2336 NAD 0.000000
> 34 NO2* -15.6630 -23.5280 11.6530 N.3 ???R??r?? 2336 NAD 0.000000
> 35 NC1* -13.5960 -24.3910 12.7910 N.3 ???R??r?? 2336 NAD 0.000000
> 36 NN1 -13.6060 -23.8090 14.1870 N.am ???R??r?? 2336 NAD 0.000000
> 37 NC2 -13.1200 -22.4490 14.3950 N.am ???R??r?? 2336 NAD 0.000000
> 38 NC3 -12.8430 -21.9970 15.6290 N.3 ???R??r?? 2336 NAD 0.000000
> 39 NC7 -12.3390 -20.5870 15.8630 N.3 ???R??r?? 2336 NAD 0.000000
> 40 NO7 -13.1040 -19.7730 16.4340 N.3 ???R??r?? 2336 NAD 0.000000
> 41 NN7 -11.1020 -20.2540 15.4620 N.am ???R??r?? 2336 NAD 0.000000
> 42 NC4 -13.0210 -22.8940 16.8600 N.3 ???R??r?? 2336 NAD 0.000000
> 43 NC5 -14.0440 -23.9900 16.5980 N.3 ???R??r?? 2336 NAD 0.000000
> 44 NC6 -14.0690 -24.5720 15.2980 N.3 ???R??r?? 2336 NAD 0.000000
> @<TRIPOS>BOND
> 1 1 2 1
> 2 1 3 1
> 3 1 4 1
> 4 1 23 1
> 5 4 5 1
> 6 5 6 1
> 7 6 7 1
> 8 6 8 1
> 9 7 12 1
> 10 8 9 1
> 11 8 10 1
> 12 10 11 1
> 13 10 12 1
> 14 12 13 1
> 15 13 14 1
> 16 13 22 1
> 17 14 15 1
> 18 15 16 1
> 19 16 17 1
> 20 16 22 1
> 21 17 18 1
> 22 17 19 1
> 23 19 20 1
> 24 20 21 1
> 25 21 22 1
> 26 23 24 1
> 27 24 25 1
> 28 24 26 1
> 29 24 27 1
> 30 27 28 1
> 31 28 29 1
> 32 29 30 1
> 33 29 31 1
> 34 30 35 1
> 35 31 32 1
> 36 31 33 1
> 37 33 34 1
> 38 33 35 1
> 39 35 36 1
> 40 36 37 1
> 41 36 44 1
> 42 37 38 1
> 43 38 39 1
> 44 38 42 1
> 45 39 40 1
> 46 39 41 1
> 47 42 43 1
> 48 43 44 1
>
> @<TRIPOS>SUBSTRUCTURE
> 1 **** 1 TEMP 0 **** **** 0 ROOT 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078