AMBER Archive (2009)

Subject: RE: [AMBER] (no subject)

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Aug 07 2009 - 10:35:32 CDT


Hi John,

It looks like the hydrogen naming for LEU residue 1 in your pdb file does
not follow the format for terminal residues correctly. Quick fix is to
remove all the H's from this residue and then let Leap add them back in.

It should then work.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Beale, John
> Sent: Friday, August 07, 2009 5:17 AM
> To: amber_at_ambermd.org
> Subject: [AMBER] (no subject)
>
> I am having difficulty processing a pdb file through leap. This is what
> I am entering and what leap is giving me:
>
>
>
> rrm = loadPdb cyclesa3.pdb
>
> Loading PDB file ./cyclesa3.pdb
>
> Created a new atom named H within residue: .R<NLEU 1>
>
> Total atoms in file: 2430
>
> Leap added 3 missing atoms according to residue templates:
>
> 3H/lone pairs
>
> The file contained 1 atoms not in residue templates
>
>
>
> saveAmberParm rrm test.prmtop test.inpcrd
>
> Checking unit.
>
> WARNING: The unperturbed charge of the unit: -5.000000 is not zero
>
> FATAL: Atom .R<NLEU 1>.A<H22> does not have a type
>
> Failed to generate parameters
>
> Parameter file was not saved.
>
>
>
> My pdb file is appended below. Can someone tell me what is wrong and
> how to correct the problem? Thanks!
>
>
>
> John

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