AMBER Archive (2007)

Subject: Re: AMBER: FATAL: Atom .R<CYF 17>.A<N 1> does not have a type.

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 05 2007 - 18:41:32 CST

On Wed, Dec 05, 2007, Boutheina Kerkeni wrote:

> But my respective lib files do not contain any H atom- compared to
> the CYF.off that you sent me (exple: HN, HA, HB3,HB2...) How did you
> include these to the .lib?

I just edited the oridinary CYS residue, removed the HG atom, and (I think)
modified the charges.

> In my case I did this:
> CYF=loadpdb cyf.pdb
> edit CYF
> and used draw bond command in xleap then
> I edited the selection, entered charges, then save and quit table
> then
> saveoff CYF cyf.lib

This will never work. A pdb file doesn't have any information about amber
atom types, and drawing in bonds doesn't add type information either. So,
nothing you have done would assign atom types. You could select all atoms,
then "edit seleted atoms" in the xleap GUI, and fill in the atom types by hand
in the spreadsheet. But my way seems simpler, especially if your cyf.pdb file
doesn't have hydrogens either.....

...dac

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