Alignment and RMSD using Marvinspace

I loaded two conformations of methotrexate in Marvinspace 5.4.0.1  generated by different software, one is by Marvinsketch. (attached)

When i try to perform an alignment by selecting:

Alignment> Rigid for all Molecules

I get the error:

Molecule count should be between 2-6 to align.

Where am i going wrong ?

Thanks in advance,

Manali

 

Hi Manali,

I suggest to align molecules in MarvinSketch:

-open the file methotrexate_lowestenergy.pdb 

-press ctrl-N for new window

-in the new window load the tmpq.pdb

-select all atoms of tmpq.pdb with ctrl-A then copy to clipboard by pressing  ctrl-C

-change back to the first MarvinSketch window then paste here the second molecule with ctrl-V

At this point you have both molecules in the same window and they will be aligned here. The molecule that has selected atoms will be rigid (its conformation won`t change) during the alignment. The conformation of the unselected one will be free to change. You can select and unselect molecules here as you want.

-Choose from the menu Tools\Conformation\3D Alignment and use the default settings by pressing OK.

one important hint:

The bond orders seems a bit messy to me in both molecules which will lead to improper alignment: I suggest to check the planar cyclohexane in tmpq.pdb (it should be aromatic) and the connecting N may have only a single bond. I would also check the planar 6 member carbon ring in the quinaziolin - like substructure.I think it is also aromatic but the N valences should also be corrected.

May check  the valences of the N atoms in the other structure. Here one may find 5-valence carbons too.

I also suggest to remove H atoms .

These modifications will lead to better alignment.

Good luck!

Adrian