VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Mon Apr 16 2007 - 20:06:58 CDT

Thanks John,
you are right. The problem is gone in 1.8.6.

John Stone escribió:
> 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
>>
>
>