[gmx-users] Error with pdb input

[Justin A. Lemkul]

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

-- 
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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

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