[PyMOL] how to keep the atom order when convert mol2 file to pdb in pymol

Fri, 12 Aug 2016 09:26:53 -0700 

Hi,

   Everyone.

   I always using pymol to prepare the pdb files for MD simulations. However, 
when I merge the extra small molecular (substrate optimized from the 
Gaussian09, mol2 formats) and the protein file (PDB formats) into the a single 
pdb, I found the atom order of substrate is not the same as the original mol2 
files.

   It seems the pymol would put the the hydrogen atom after the heavy atom. It 
also rearrange the atom when convert the mol2 file to mol2 file when using the 
pymol. (The attachments, from the test1 to test2 by using pymol)

   However the rearrangement of the atom is not very convenient for the 
following actions. I wonder how to keep the original atom order when convert to 
other formats by using pymol. （I using PYMOL 1.7.0 in Ubuntu 14.04）

   Thanks very much.

                                                        Chen

Attachment: test2_from_pymol.pdb
Description: Binary data

Attachment: test2_from_pymol.mol2
Description: Binary data

Attachment: test1.mol2
Description: Binary data

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