AMBER Archive (2009)

Subject: Re: [AMBER] atom types in pdb files

From: Dan Kaps (dan.kaps_at_yahoo.com)
Date: Mon Apr 13 2009 - 14:29:43 CDT

The residue names match those in the .prepin files; however, the atom names to not. Unfortunately the atoms in the .prepin files are in different orders than those in the .pdb files...what a mess...any suggestions?

________________________________
From: Kristina Furse <Kristina.Furse.1_at_nd.edu>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Monday, April 13, 2009 12:30:05 PM
Subject: RE: [AMBER] atom types in pdb files

Looks like your "residue" doesn't have a name--see where it says "UNK" in the error message? If you name the residues (and all of the atoms...) in your pdb file so the names match the .prepin files you should be OK.

K 

--
Kristina Furse
Postdoctoral Research Associate
262 Stepan Chemistry Hall
Notre Dame, IN 46556
(574)631-3904

________________________________________
From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of Dan Kaps [dan.kaps_at_yahoo.com]
Sent: Monday, April 13, 2009 10:23 AM
To: amber_at_ambermd.org
Subject: [AMBER] atom types in pdb files

Hello All,
I'm having trouble saving saving .prmtop and .inpcrd files in tleap after loading a .pdb file.  I use the command MOL = loadpdb myfile.pdb however, when I do check MOL i get the error message: "FATAL:  Atom .R<UNK 1>.A<C1 1> does not have a type.
" for every atom in my .pdb file.  (I also get the same error message after loading all the necessary .prepin and .frcmod files and attempting to save the .prmtop and .inpcrd files)  Does anyone know what I have to do to fix this issue?  There ARE two residues in this .pdb file and I have never had this problem when using a pdb with just one residue so that might have something to do with it.  (I don't know much about .pdb files, my group is a bunch of physicists using amber for something other than what was intended\).
Thanks,
Dan

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