MOL to PDB format

Hi! I would like to know two points:

1. Is MarvinSketch able to save ligands in .pdb or .mol2 format?

2. is MarvinSketch able to calculate protonation and add Hydrogens in 3D ligands structures?

Thanks for your answers.

Dhoha

Hello,

Yes for both is the answer!

Best,

Krisz

Hi Krisz,

my aim is to add Hydrogens to my ligands. I extracted HETATM lines from the RCSB PDB and I saved my ligand file in pdb format ligand.pdb.
I could not add Hydrogens with command lines, thus I converted my file into sdf file with "molconvert" to have ligand.sdf, then I used the command:

"ChemAxon/MarvinBeans/bin/cxcalc majormicrospecies -M 7.4 ligand.sdf -f sdf:H > ligand.sdf"

I tried wth different format but I always have the error message:

chemaxon.formats.MolFormatException: Cannot read molecule file.
    at chemaxon.formats.MolInputStream.init(MolInputStream.java:146)
    at chemaxon.formats.MolInputStream.<init>(MolInputStream.java:115)
    at chemaxon.formats.MolImporter.init(MolImporter.java:542)
    at chemaxon.formats.MolImporter.<init>(MolImporter.java:118)
    at chemaxon.marvin.Calculator.run(Calculator.java:1347)
    at chemaxon.marvin.Calculator.main(Calculator.java:2078)
Caused by: chemaxon.formats.MolFormatException: Cannot recognize format ([]?)
Unrecognized file contents:
7.4...

    at chemaxon.formats.recognizer.RecognitionSubsystem.getFormat(RecognitionSubsystem.java:324)
    at chemaxon.formats.MolInputStream.initTextFormat(MolInputStream.java:292)
    at chemaxon.formats.MolInputStream.init(MolInputStream.java:135)
    ... 5 more

Do you know what is the best command line to add Hydrogens to pdb files containing HETATM lines?

Thank you for your help.

Dhoha

Hi Dhoha,

 

You can add Explicit Hydrogens via molconvert too.

You should use molconvert sdf:H input.sdf -o output.sdf.

 

I recommend using different files as input and output.

BRs

Peter

Hi Peter,

actually I would like to have only polar Hydrogens at pH=7.4. I need this before launching a docking. The molconvert command adds all Hydrogens.

Thanks again.

Regards.

Dhoha

Hi, 

Unfortunately there is no way to add just those Hs that are polar. Molconvert can't do that. 

Daniel

Hi Daniel,

yes exactly, but the command cxcalc majormicrospecies adds polar H. I would like to know what is wrong with what I wrote "cxcalc majormicrospecies -M 7.4 ligand.sdf -f sdf:H > ligand.sdf" because I have the same error message:

chemaxon.formats.MolFormatException: Cannot read molecule file.
    at chemaxon.formats.MolInputStream.init(MolInputStream.java:146)
    at chemaxon.formats.MolInputStream.<init>(MolInputStream.java:115)
    at chemaxon.formats.MolImporter.init(MolImporter.java:542)
    at chemaxon.formats.MolImporter.<init>(MolImporter.java:118)
    at chemaxon.marvin.Calculator.run(Calculator.java:1347)
    at chemaxon.marvin.Calculator.main(Calculator.java:2078)
Caused by: chemaxon.formats.MolFormatException: Cannot recognize format ([]?)
Unrecognized file contents:
7.4...

    at chemaxon.formats.recognizer.RecognitionSubsystem.getFormat(RecognitionSubsystem.java:324)
    at chemaxon.formats.MolInputStream.initTextFormat(MolInputStream.java:292)
    at chemaxon.formats.MolInputStream.init(MolInputStream.java:135)
    ... 5 more

Thanks again.

Dhoha

Hi, 

The command parameter M is for setting the tautomerization during the microspecies calculation. The 7.4 value for this option is not right. I guess you wanted to set the pH value; in that case you should use the -H option instead. So e.g. type

cxcalc majormicrospecies -H 7.4 aspirine -f sdf:H

I hope this helps. 

Daniel

Hi Daniel,

thanks for your help! It's exactly the same command as "molconvert sdf:H input.sdf -o output.sdf", it adds all hydrogens. What I wanted to do is to add polar Hydrogens only.

Dhoha

Hi, 

You can't add just polar Hs as we can't apply a filter when adding Hs to a molecule.

Daniel

Thank you very much for your answers!! It helps a lot!

Dhoha