[gmx-users] Problem with pdb2gmx in gromacs 4.5.3

[Justin A. Lemkul]

Tomy van Batis wrote:
> Dear Gromacs users
> 
> I have a very strange problem when using pdb2gmx in the gromacs 4.5.3. I 
> looked up the mailing list but I can't find something similar.
> 
> I have in a .pdb file a crystalline substrate consisting of Si particles.
> 
> By running in previous gromacs version (i.e. gromacs 3.3) :
> 
> /pdb2gmx -f name.pdb -p topol.top -o output.gro
> /
> I get the following result for the /*topol.top* /file*:*
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  
> typeB    chargeB      massB
>      1         SI      1    ZZZ     D1      1          0      28.08   ; 
> qtot 0
>      2         SI      1    ZZZ     D2      2          0      28.08   ; 
> qtot 0
>      3         SI      1    ZZZ     D3      3          0      28.08   ; 
> qtot 0
>      4         SI      1    ZZZ     D4      4          0      28.08   ; 
> qtot 0
>      5         SI      1    ZZZ     D5      5          0      28.08   ; 
> qtot 0
> etc
> 
> which of course is normal, but by doing the same in gromacs 4.5.3,  the 
> */topol.top /*file*/ /*is the following:
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  
> typeB    chargeB      massB
> ; residue   1 ZZZ rtp ZZZ  q  0.0
>      1         SI      1    ZZZ     D1      1          0      28.08   ; 
> qtot 0
>      2          O      1    ZZZ     D2      2          0 1.48594e-41   ; 
> qtot 0
>      3          O      1    ZZZ     D3      3          0 1.48594e-41   ; 
> qtot 0
>      4          O      1    ZZZ     D4      4          0 1.48594e-41   ; 
> qtot 0
>      5          O      1    ZZZ     D5      5          0 1.48594e-41   ; 
> qtot 0
> etc
> 
> I have no idea where these O come from.
> 
> Did anyone have similar problems?
> 

This bug was fixed months ago.  Please upgrade to 4.5.4 and try again.

-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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