Differences in conformers calc. MarvinSketch / cxcalc

User 25d107bd42

23-03-2009 08:28:33


while evaluating the five Clean3D methods (see ftopic.4656) I tried to calculate all conformers of several molecules. Having now problems with the command line tool I will post here the first problem with a very simple example:


MarvinSketch produces three conformers: 4.63 kcal/mol (C-C-C-C trans), 5.38 kcal/mol (C-C-C-C gauche left-hand) and 5.38 kcal/mol (C-C-C-C gauche right-hand). Number 2 and 3 have of course the same energy, these are "image" and "mirror image".

BTW: To have this feature is a super option of MarvinSketch, we like to use it in teaching.

But using "cxcalc conformers" I get only one conformer, the most stable one. I use:

cxcalc -o n-Butane-Confs.sdf  conformers  -m 1000  -d 0.1  -s true  -e true  -y true  -l 1000 -O 3  n-Butane.mrv

but mview n-Butane-Confs.sdf contains only one conformer.

What's wrong ?

Regards, Hans-Ulrich

User 25d107bd42

23-03-2009 19:10:50

Hi, I found my failure.

In the command line above there is "-s true" and according to "cxcalc conformers -h" this means:

  -s, --saveconfdesc    [true|false] if true a single conformer is saved

                        with a property containing conformer information

                        (default: false)

Using the following command line with the default "-s false" produces the same result as the Marvinsketch GUI, i.e. the three conformers expected for n-Butane.

cxcalc -o n-Butane-Confs.sdf conformers -m 1000 -d 0.1 -s false  -e true -y true -l 1000 -O 3 n-Butane.mrv

The text "a single conformer is saved" means obviously the lowest energy conformer is saved.

Now I can measure the time the conformer calculations consume.

Please excuse me for producing unnecessary work.

Regards, Hans-Ulrich

User 25d107bd42

24-03-2009 09:07:56

Hi Marvin documentation writers,

a little comment on my problem posted above. I simply read over the tiny "a" (indefinite article?) in the directions for use:

  -s, --saveconfdesc    [true|false] if true a single conformer is saved

                        with a property containing conformer information

                        (default: false)

Now I know this "a" means "one". But then there comes the question: Which one?

I suggest to write: "... if true only the lowest energy conformer is saved ..." (According to my tests exactly this is done.)

Regards, Hans-Ulrich

ChemAxon 8b644e6bf4

26-03-2009 02:37:26

Dear Hans-Ulrich,

Thanks for the suggestion about the clarification.