[Chimera-users] Converting SDF files to Mol2 Format

[Eric Pettersen]

On Mar 26, 2010, at 8:15 AM, Nancy wrote:

> Hi Elaine,
>
> I need to convert a large number of PubChem SDF files into Mol2  
> format.  When I convert an SDF file into Mol2 format, I add partial  
> charges and run energy minimisation on the molecule, as this is  
> necessary for the program I am inputting the files into.  So far, I  
> have only used Chimera in this method to convert individual files.   
> Is there a way to convert a large number of SDF files to Mol2 format  
> at once, and also preserve the filenames?
>
> Thanks in advance,
>
> Nancy

Hi Nancy,
	There are several possibilities here.  Probably the most  
straightforward is to use either the 1.4 or 1.4.1 release in  
conjunction with a script to process your files.  Let's assume your  
files are all in one directory and have names of the form  
moleculeName.sdf .  The following csh-style script would accomplish  
the task:

#!/bin/tcsh -f
foreach sdf (*.sdf)
	echo $sdf
	chimera --nogui $sdf processSDF.cmd
	mv output.mol2 $sdf:r.mol2
end

and where the contents of "processSDF.cmd" is just:

minimize
write format mol2 0 output.mol2

You would want to put the csh script in a file (e.g. processSDF.csh)  
which you would want to make executable (chmod +x processSDF.csh).   
You would want to run the script in the directory with the SDF files,  
where the processSDF.cmd file would also be located.  If you are  
familiar with shell scripting you can of course add paths to the  
various script names to change these requirements.
	The above, though simple, may be a little slow due to starting one  
instance of Chimera per SDF file.  You can get Chimera to run through  
your directory of SDF files, but you have to use a Python script  
instead of a Chimera command script.  Like this:

chimera --nogui processSDF.py

with the contents of processSDF.py being:

from os import chdir, listdir
from chimera import runCommand
chdir("/path/to/SDF-file-dir") # change to the SDF file directory
for sdf in listdir("."):
	if not sdf.endswith(".sdf"):
		continue
	runCommand("open " + sdf)
	runCommand("minimize")
	runCommand("write format mol2 0 " + sdf[:-4] + ".mol2")
	runCommand("close all")

	You could do all the above in the 1.5 release but the issue is that  
the 1.5 branch now uses the 1.3 version of AmberTools/Antechamber  
which relies on the program sqm to compute charges rather than mopac.   
While the charges computed by sqm are theoretically more precise than  
mopac, they take considerably longer to compute.  We intend to add  
options for using less strict charge-convergence criteria in order to  
speed things up, but that work still is yet to be done.  So whereas  
moieties involving ~35 or less atoms (including hydrogens) don't take  
excessive amounts of time (30 seconds or less), the compute time  
scales with the cube of the number of atoms(!) so a system of 72 atoms  
took more than 13 minutes and a system of 84 atoms took more than 21  
minutes.  I've also found that sqm fails to converge sometimes.  The  
only structure I've had this happen with is ATP (at -4 charge), but it  
happened for a variety of conformers of ATP.
	A final possibility is to use the PubChem3D (PubChem3D release note)  
files and convert them directly to Mol2 files.  This would require the  
1.5 release (the 1.4 series doesn't read the charges in the SDF file)  
and assumes that the included MMFF charges are sufficient for your  
needs and that the conformer provided is good enough for your purposes  
without minimization.  Using minimization would defeat the purpose  
here since Chimera's minimization needs to know GAFF atom types which  
requires non-standard residues to be processed by Antechamber which  
will add charges in addition to assigning types.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


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