AMBER Archive (2007)

Subject: RE: AMBER: PDB files

From: Hayden Eastwood (s0237717_at_sms.ed.ac.uk)
Date: Mon Apr 30 2007 - 12:12:01 CDT

Dear John

The nomenclature that amber uses for pdb files is different to that of the
standard brookhaven format. To convert a brookhaven format to that of amber
(so leap can read it) you must use the "protonate" command as follows:
 
protonate -i input.pdb > output.apdb

Where input.pdb is the standard brookhaven format and where output.apdb is
the reformatted amber pdb file. This should then read into leap without any
problems. However, it's important to check the sanity of every pdb file
before and after the protonate command is implemented. For example if you
have a disulfide bridge you will manually have to change each of the residue
pairs within the pdb file from CYS to CYX. A similar process is sometimes
required to get the right protonation state for a given peptide.

I hope that helps.

Hayden

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