conformers and dreidingnergy

User 1bf9422018

29-03-2008 21:19:29

Dear all,

I have generated conformers for a molecule using cxcalc:

cxcalc -v -o cadr.sdf conformers \

  --format sdf \

  --saveconfdesc false \

  --prehydrogenize false \

  --maxconformers 100 \

  --diversity 0.1 \

  --timelimit 1800 \

  --hyperfine false \

  --optimization 1 \


To get a list of the energy of each conformer, I found easier to run cxcalc on the newly created cadr.sdf file:

cxcalc -v dreidingenergy -l never cadr.sdf > out.txt

than trying to get the values from the cadr.sdf file. However, the values are not identical... Is this expected? Am I using the wrong options in dreidingenergy?

I'm running cxcalc version 5.0.1 in Mac OS X 10.4.10.


Rui Rodrigues

ChemAxon 8b644e6bf4

31-03-2008 12:26:48

Dear Rui Rodrigues,

Probably your input molecule has implicit H atom(s). During conformer generation these implicit H atoms are made temporarily explicit. When "--prehydrogenize false" specified, these temporal H atoms are removed AFTER Dreiding energy calculation, so the stored energies are interpreted on the hydrogenized structure.

The second, "dreidingenergy" calculation is invoked on 3D structures having no explicit H atoms, so probably this led to the differing energies.

You should use "--prehydrogenize true" for the conformational analysis to preserve the hydrogen atoms for further calculations.

If you have any further questions, feel free to ask them,



User 1bf9422018

31-03-2008 18:50:48

Dear Gabor,

Thanks for your reply. I think the H atoms in my input molecule are all explicit... Please find attached my input file. If the H atoms are indeed all explicit, it is OK to use prehydrogenize false during conformer generation? I tried to make an input file with explicit H atoms to make sure the phosphate groups remained charged...

ChemAxon 8b644e6bf4

01-04-2008 12:57:27

Dear Rui Rodrigues,

Thanks for the original structure. You are right, all of the H atoms are explicit, so you can use "--prehydrogenize false".

My second guess would be that usage of "sdf" format probably could cause such minor differences because this format stores coordinates using four fractional digit precision. However the differences were reproduced using "mrv" format.

The energy values using "mrv" format should be identical so I will examine this problem and will keep you informed in this topic.



ChemAxon 8b644e6bf4

02-07-2008 18:31:38

Dear Rui Rodrigues,

We will introduce major modifications in the upcoming 5.1 version. (It will be released in a few days.) The energy calculation code is restructured and provides consistent results. (These may differ from the energies calculated by the old implementation.)