AMBER Archive (2005)

Subject: Re: AMBER: problem with protein ligand complex

From: David A. Case (case_at_scripps.edu)
Date: Sat Jul 16 2005 - 14:05:02 CDT

On Sat, Jul 16, 2005, Claire Zerafa wrote:
>
> i am using amber for the first time, and I am trying to model a protein
> ligand complex in xleap- specifically to generate .prmtop and .inpcrd files.
> I have prepared .prepin and .frcmod files, and read the complex into xleap
> with no errors I could see.

I don't see any errors either...your output looks fine. (But see the note
about disulfide bonds.)

>
> the prmtop and inpcrd files generate incompletely is they have that funny
> round icon on the SGI. Also, the residues- CTHR, NCYX and WAT above do not
> feature in the pdb file, the .prepin file or the frcmod file, so i dont know
> where they come from.

The icons that SGI may assign to files have nothing to do with Amber at all.
CTHR is a C-terminal THR, and NCYX is an N-terminal cysteine: these names
are given by amber. Amber also by default renames HOH residues to "WAT".

Remember that you must manually specify any disulfide bonds in your structure
using the "bond" command -- this is *not* done automatically.

...dac

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