AMBER Archive (2008)

Subject: Re: AMBER: unable to open pdb file

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Dec 04 2008 - 05:41:32 CST

On Wed, Dec 03, 2008, Taufik Al-Sarraj wrote:
>
> I am unable to open a pdb file in molmol, the error message is
> unknown residues: DA, DC, DG, DT, HIE, Na+
> unknown atoms: OXT (ARG+), OXT (GLU), H1, H2, H3 (LYS+), H1, H2, H3 (MET)

You probably want the -bres option (to get Brookhave, aka pdb) residue names.
Don't use the -aatm flag, since that gives Amber names, not Brookhaven ones.

If molmol doesn't like OXT or H1,H2,H3 (terminal residues) you should change
those by hand. Of course, you can always change all of the things molmol
doesn't like by hand.

...dac

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