[AMBER] problems with added hydrogens to non standard residue

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From: Urszula Uciechowska <urszula.uciechowska.chem.umu.se>
Date: Mon, 14 May 2012 10:26:00 +0200

Dear Amber users,

I have a peptide with a non standard amino acid, parameters/lib were prepared using RED server. After loading this peptide into the xleap, program added hydrogens in strange conformations (residue name is MGR and the H atoms H4, H2 connected to C3 and H1,H3 connected to C2. I attached the pdb file. Could someone tell me what is wrong here? or how to correct it?

thank you in advance

/Urszula

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chemical/x-pdb attachment: peptide_amber.pdb

Received on Mon May 14 2012 - 01:30:03 PDT