How to generate 3D multiple conformation using molconvert

Dear Sirs,





I would like to generate the 3D conformations for my molecules in batch mode (molconvert on LINUX). The idea here is to build a set of conformations for each molecule (let say 100 or 1000 conf per ligand). I am trying with [writeconfs] and [fm] for specificatin of number of conformations but it is not working (all numbers such as 10, 100, 1000, 10000 in fm are producing the same output, namely two structures ! instead of 100/1000/10000):





molconvert -3:[E][writeconfs]{1a42_confs}[fm]{100} sdf 1a42.smi -o 1a42.sdf





How can I specify the exact number of conformations which will be writen to the output file ?





I will appreciate your help very much ....





Kind regards





Dariusz

Dear Dariusz,





Please, read carefully the help, via molconvert -H3D, since you should add not only one single number after [fm] but use it three times, since three different limits exist during the process for different tasks. Also, please, provide an example structure, because it might not have more than 2 stable conformers. Molecular dynamics simulations are the right tool for finding multiple and not necessarily stable conformations of molecules. Providing such a tool in the framwork of Marvin is in progress and will be available soon.





Best wishes,





Ödön

darman wrote:

Dear Sirs, I would like to generate the 3D conformations for my molecules in batch mode (molconvert on LINUX). The idea here is to build a set of conformations for each molecule (let say 100 or 1000 conf per ligand). I am trying with [writeconfs] and [fm] for specificatin of number of conformations but it is not working (all numbers such as 10, 100, 1000, 10000 in fm are producing the same output, namely two structures ! instead of 100/1000/10000): molconvert -3:[E][writeconfs]{1a42_confs}[fm]{100} sdf 1a42.smi -o 1a42.sdf How can I specify the exact number of conformations which will be writen to the output file ? I will appreciate your help very much .... Kind regards Dariusz

Dear Ödön,





I have tried both - with 3 number and with 1 number after [fm] - I am getting only 2 molecules anyway :) Maybe you are right that there are only two stable conformations - but personaly I do not believe it -> one can see the possibility of rotating the second chemical group, also the rotated group can have more than provided two conformations.





The strange thing is that running multiplicity "1":


molconvert -3:{fine}[E][fm]{1}{1}{1}[writeconfs]{conf_1a42} sdf 1a42.smi -o conf_1a42.sdf


I am getting 3 structures in conf_1a42.0.mol whereas runing the multiplicity "10" I am getting only 2 structures:


molconvert -3:{fine}[E][fm]{10}{10}{10}[writeconfs]{conf_E2_1a42} sdf 1a42.smi -o conf_E2_1a42.sdf





Any ideas ?





Anyway - thanks for your help :)








The example is as follows:





1a42.smi


c1(sc2c(c1)[C@@H]([NH2]CC)C[N@](CCOCC)S2(=O)=O)S(=O)(=O)N





The real mol 3D conformation:





1a42.mol:

Code:

1a42_ligand  OpenBabel03030615263D  45 46  0  0  0  0  0  0  0  0999 V2000    -4.1878    5.0652   12.2705 H   0  0  0  0  0    -2.5023    5.6279   12.5332 H   0  0  0  0  0    -5.4450    2.0670   16.0490 C   0  0  0  0  0    -3.3940    5.2050   13.0190 C   0  0  0  0  0    -3.0550    3.8670   13.7100 C   0  0  0  0  0    -3.3490    7.4080   13.9350 C   0  0  0  0  0    -2.0760    7.4260   14.7640 C   0  0  0  0  0    -1.9150    9.7690   15.0590 C   0  0  0  0  0    -0.8780   10.9030   15.1780 C   0  0  0  0  0    -5.4250    0.9940   18.2870 O   0  0  0  0  0    -7.3980    0.8170   16.9950 O   0  0  0  0  0    -5.4860   -0.5450   16.4610 N   0  0  0  0  0    -5.9660    0.7500   16.9970 S   0  0  0  0  0    -4.3210    2.1520   15.2920 C   0  0  0  0  0    -4.1650    3.3450   14.6420 C   0  0  0  0  0    -5.2160    4.2000   14.9310 C   0  0  0  0  0    -6.3790    3.5010   15.9790 S   0  0  0  0  0    -5.2950    5.8270   14.3680 S   0  0  0  0  0    -6.1600    5.8730   13.2440 O   0  0  0  0  0    -5.8580    6.6800   15.3730 O   0  0  0  0  0    -3.8480    6.0650   14.0900 N   0  0  0  0  0    -2.7760    2.8950   12.6490 N   0  0  0  0  0    -1.3070    8.5960   14.5330 O   0  0  0  0  0    -1.5640    3.0110   11.8410 C   0  0  0  0  0    -1.4630    1.9270   10.7540 C   0  0  0  0  0    -2.1480    4.0091   14.3160 H   0  0  0  0  0    -4.0746    8.1411   14.3171 H   0  0  0  0  0    -3.1307    7.6244   12.8788 H   0  0  0  0  0    -1.4701    6.5457   14.5033 H   0  0  0  0  0    -2.3456    7.3831   15.8296 H   0  0  0  0  0    -2.3272    9.5486   16.0547 H   0  0  0  0  0    -2.7265   10.0886   14.3888 H   0  0  0  0  0    -1.3631   11.8021   15.5858 H   0  0  0  0  0    -0.4651   11.1282   14.1836 H   0  0  0  0  0    -0.0657   10.5881   15.8496 H   0  0  0  0  0    -5.7251   -1.4044   16.9303 H   0  0  0  0  0    -3.6030    1.3374   15.2093 H   0  0  0  0  0    -3.5545    2.9328   12.0099 H   0  0  0  0  0    -2.7454    1.9882   13.0880 H   0  0  0  0  0    -0.6906    2.9254   12.5041 H   0  0  0  0  0    -1.5597    3.9975   11.3543 H   0  0  0  0  0    -0.5339    2.0668   10.1820 H   0  0  0  0  0    -2.3260    2.0056   10.0765 H   0  0  0  0  0    -1.4568    0.9336   11.2263 H   0  0  0  0  0    -4.9248   -0.5665   15.6336 H   0  0  0  0  0   4  1  1  0  0  0   4  2  1  0  0  0   3 17  1  0  0  0   3 14  2  0  0  0   3 13  1  0  0  0   5  4  1  0  0  0   4 21  1  0  0  0  15  5  1  0  0  0   5 22  1  0  0  0   5 26  1  0  0  0  21  6  1  0  0  0   6  7  1  0  0  0   6 27  1  0  0  0   6 28  1  0  0  0   7 23  1  0  0  0   7 29  1  0  0  0   7 30  1  0  0  0  23  8  1  0  0  0   8  9  1  0  0  0   8 31  1  0  0  0   8 32  1  0  0  0   9 33  1  0  0  0   9 34  1  0  0  0   9 35  1  0  0  0  13 10  2  0  0  0  13 11  2  0  0  0  13 12  1  0  0  0  12 36  1  0  0  0  12 45  1  0  0  0  14 15  1  0  0  0  14 37  1  0  0  0  15 16  2  0  0  0  18 16  1  0  0  0  16 17  1  0  0  0  21 18  1  0  0  0  18 20  2  0  0  0  18 19  2  0  0  0  22 24  1  0  0  0  22 38  1  0  0  0  22 39  1  0  0  0  24 25  1  0  0  0  24 40  1  0  0  0  24 41  1  0  0  0  25 42  1  0  0  0  25 43  1  0  0  0  25 44  1  0  0  0 M  END $$$$

Dear Dariusz,





Try something like:


molconvert -3:[prehydrogenize]S0[ca][fm]{500}{500}{500}[writeconfs]{conf_1a42} sdf 1a42.smi -o conf_1a42.sdf





I've got 300 conformers this way in the file named "conf_1a42.0.mol"





Best wishes,





Ödön

darman wrote:

Dear Ödön, I have tried both - with 3 number and with 1 number after [fm] - I am getting only 2 molecules anyway :) Maybe you are right that there are only two stable conformations - but personaly I do not believe it -> one can see the possibility of rotating the second chemical group, also the rotated group can have more than provided two conformations. The strange thing is that running multiplicity "1": molconvert -3:{fine}[E][fm]{1}{1}{1}[writeconfs]{conf_1a42} sdf 1a42.smi -o conf_1a42.sdf I am getting 3 structures in conf_1a42.0.mol whereas runing the multiplicity "10" I am getting only 2 structures: molconvert -3:{fine}[E][fm]{10}{10}{10}[writeconfs]{conf_E2_1a42} sdf 1a42.smi -o conf_E2_1a42.sdf Any ideas ? Anyway - thanks for your help :)

Dear Dariusz,





You can also try our new conformer plugin, which is already available in the 4.1 alpha release of Marvin. You can try it (as applet) or download it from here: http://www.chemaxon.com/shared/alpha





The conformer generation can be done trough command line interface (cxcalc tool) or trough graphical interface (Marvin).





The command line way (example, using your input file):

Code:

cxcalc conformers -m 250 -f sdf 1a42.smi > conformers_1a42.sdf

It generates 250 conformers (or less, if there are no 250 conformers) of the molecule(s) given in the input file (1a42.smi). The conformers are written to file conformers_1a42.sdf.





For the available options see

Code:

cxcalc conformers -h

The graphical interface can be accessed from Marvin's menu: Tools->Conformers. The previously mentioned applet can be accessed here: http://www.chemaxon.com/shared/alpha/marvin/sketch.html





Best regards,


Zsolt

Thanks for explanation. It is working now as I would like it to work!





Regards





Dariusz

Zsolt wrote:

Dear Dariusz, You can also try our new conformer plugin, which is already available in the 4.1 alpha release of Marvin. You can try it (as applet) or download it from here: http://www.chemaxon.com/shared/alpha The conformer generation can be done trough command line interface (cxcalc tool) or trough graphical interface (Marvin). The command line way (example, using your input file): Code: cxcalc conformers -m 250 -f sdf 1a42.smi > conformers_1a42.sdf It generates 250 conformers (or less, if there are no 250 conformers) of the molecule(s) given in the input file (1a42.smi). The conformers are written to file conformers_1a42.sdf. For the available options see Code: cxcalc conformers -h The graphical interface can be accessed from Marvin's menu: Tools->Conformers. The previously mentioned applet can be accessed here: http://www.chemaxon.com/shared/alpha/marvin/sketch.html Best regards, Zsolt