[gmx-users] Error with pdb input

[Justin A. Lemkul]

Please keep the discussion on the list.

Lara Bunte wrote:
> Hi
> 
> what is wrong in the format or what do I have to change. Please don't 
> give me a link to the pdb site, I do not understand it :-(
> 

The PDB format requires certain columns with the prescribed information be 
present at the specified spacing.  Since you won't allow me to point you to the 
site that has the walkthrough on how to interpret the contents, then the best I 
will offer you is to download any protein structure from the PDB and look at it. 
  You will see dramatic differences between the required format and what you 
have attempted to use.  A small example is available in the online manual, but 
opening the files in a text editor to clearly see the spacing is preferred.

http://manual.gromacs.org/online/pdb.html

-Justin

> regards
> Lara
> 
> 
> ------------------------------------------------------------------------
> *Von:* Justin A. Lemkul <jalemkul at vt.edu>
> *An:* Lara Bunte <lara.bunte at yahoo.de>; Discussion list for GROMACS 
> users <gmx-users at gromacs.org>
> *Gesendet:* 19:02 Mittwoch, 9.November 2011
> *Betreff:* Re: [gmx-users] Error with pdb input
> 
> 
> 
> Lara Bunte wrote:
>  > Hello
>  >
>  > I got the following error (my command is pdb2gmx -f coord.pdb -water 
> tip3p ) :
>  >
>  > Warning: Number of atoms in coord.pdb is 0
>  >
>  > Software inconsistency error:
>  > Trying to deduce atomnumbers when no pdb information is present
>  >
>  >
>  > My pdb file has the following structure
>  >
>  > HEADER my molecules name
>  > ATOM 1    5.33618975678115    -0.07916062770658      
> 1.39429663262701      n
>  > ATOM 2    6.73371782109540    -2.15676333272371      
> 0.62908982963763      c
>  > ATOM 3    9.03483733311025    -2.20332618463802      
> 0.65509246122614      o
>  > ATOM 4    5.38645647191591    -4.30702600755030    -0.22693721129824  
>     n
>  > ATOM 5    2.79934580695015    -4.52186897159807    -0.44786509349390  
>     c
>  > ATOM 6    1.68306568299327    -6.40460311779204    -1.24068079528474  
>     o
>  > ATOM 7    1.48545702127742    -2.26124629061096      
> 0.37342878111953      c
>  >
>  > The numbers are cartesian coordinates in Bohrs
>  >
> 
> The file does not follow standard PDB format, which is required by all 
> Gromacs programs to function properly.
> 
> -Justin
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================