Im looking for software that can help me build peptides. I need something that can synthesize using a variety of different modified amino acids, not just the 20. So that I can add molecules like hydroxyproline or selenocystein to the chain without having to manually add the hydroxides and selenium. I also need this to have the option to save files in a PDB format that is readable to PDB readers like the one CHARMM-GUI has.
I've tried Avogadro but I'm having errors in my MD simulations and I'm suspecting it the culprit. The main issue being adding 30+ amino acids and modifying most of them to be hydroxyproline by hand becomes tiresome after a while and produces errors.
Anyone have a suggestion?
Your problem is that most programs rely on an internal dictionary of the canonical amino acids to represent a peptide/protein. Any modified amino acid that is not in this dictionary has to be treated as a foreign object (HETATM in the pdb), and you need to explicitly specify in ways that are appropriate to the specific program you are using how the atoms are connected, what rotamers are allowed, the forcefield parameters for the atoms in this residues.
For some modified residues and compliant programs, "dictionary extensions" are available as Plug-ins or Force-field parameter packages, that contain the descriptions for modified and non-natural amino acids, e.g. SwissSidechain https://www.swisssidechain.ch and Vienna-PTM http://vienna-ptm.univie.ac.at
Not exactly a full solution that you're hoping for, but you can try using PeptideBuilder:
https://github.com/clauswilke/PeptideBuilder/tree/master/PeptideBuilder
It doesn't support anything beyond the canonical 20 amino acids, but you could easily fork it to extend it with the residues you require, based on bond angles etc. from the SwissSideChain (see above answer) package.
I suggest you to do this with Avogadro program, because it is Very easy، and then xonvert it to pdb formula into another program.
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