Problem with custom amino acids

Hello,

Please can anyone tell me whether there is a way to turn off the automatic addition of an OH group to the C-terminal amino acid when a custom amino acid is added to the custom dictionary?

I am adding Alanine C-amide as a custom amino acid and the result is a 5-valent acyl Carbon as seen in the attached image.

Since I have defined it as a custom amino acid then maybe you can only define acids? If so can someone tell me how I can programmatically add an amide of an amino acid?

 

Thank you.

Tim Mowlem

 

Hi,

Please describe how you extended the template library with the modified aminoacid; I mean did you modified an original record in an existing template file, or added a new record to an original template file, or created a new template file by your own?

Thank you and best regards,

Akos

Hello Akos,

I added entries to the file <userhome>/.chemaxon/custom_aminoacids.dict

Example:

X(AmN) X(AmN) [NH2][CX4](=O)[CH2][C@H]([NX3])C(=O)[NH2] 6 7

 

You can see I have added [NH2] to the end.

This procedure is described in the help page for the peptide file format at URL:

http://www.chemaxon.com/marvin/help/formats/seq-doc.html

 

Thanks.

Tim Mowlem

Hi Tim,

Marvin expects amino acid entries in the custom_aminoacids.dict file, and therefore automatically adds an OH to the second attachment point.

Best regards,

Akos

Hi Akos,

Okay I guess this is bending it a bit too far.

 

Thanks,

Tim

Can you suggest the simplest way to achieve the same end in that case i.e programmatically via the marvin api?

If we build up a chemical structure in the "peptide" format and have marvin infer the full chemical structure (i.e we have a "Molecule" Object), we want the C-terminal position to be an "amide" rather than an amino acid sometimes .

One approach would be to post-process the structure once marvin has inferred the full chemical structure from a "peptide" and turn the C-terminal OH --> NH2 programmatically via the API. Any pointers / example code would be appreciated.

I have a work-around for now which is un-elegant, but would welcome suggestions as to the best approach to take.

We have a marvin licence - is this the best way to receive support? The answer may well be of interest to other marvin users.

many thanks

Hello,

We are sorry for the late answer. Please find the attached example code to turn the C-terminal OH --> NH2 via API.

Best regards,

Erika