[gmx-users] fatal error [using pdb2gmx]

Erik Lindahl lindahl at sbc.su.se
Tue Oct 18 20:13:28 CEST 2005


On Oct 18, 2005, at 7:36 PM, Sven Huttenhouse wrote:

> Many thanks Dr. Erik for your help.
> I still have some doubts about atoms naming. in the file  
> ffG43a1.rtp I find CA sometimes represent  a carbon in a CH2 group  
> and sometimes a carbon in a CH ??
> Sometimes find numbers used to distinguish between atom from the  
> same type and sometimes letters, like HA1 HA2 or O1 O2 O3 and  
> sometimes CA CB CD representing carbon in a CH2 group??
> Is there any source where I can find the explanation of atoms naming?
> Also I'm trying to find a source that explains the pdb file format.
> I will really appreciate it is someone can guide me in how to  
> construct a pdb file for any molecule like if I want to write my  
> own pdb file for Glycine.

That would be IUPAC (International union of pure and applied  
chemistry). Since the ASCII character set doesn't contain greek  
glyphs we use CA=alpha carbon, CB=beta carbon, CG=gamma carbon,  
CD=delta carbon, etc.

Please not that there are two different concepts:

1. The name of an individual ATOM. Each atom in a molecule should  
have a unique name.
2. The name of the atomtype in the forcefield used.


Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214

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