[gmx-users] problem with gromcas 4.5.3

[Justin A. Lemkul]

leila separdar wrote:
> I have installed gromacs version 4.5.3. when I want to use pdb2gmx for 
> generating .top and .gro files for 1000 argon atoms, in topology file I 
> have seen another atom O with mass 1.48594e-41 as below I do not know 
> what to do.I do not confront with such problems when I had 4.0.7 version 
> of gromacs. please help me. also I have used gromos43a1 force feild.

Sounds like it's related to (or the same as) a known issue:

http://redmine.gromacs.org/issues/618

Note that, for a monoatomic species (or any single molecule, really) pdb2gmx is 
not necessary.  Writing a simple "argon.itp" containing the one atom and its 
nonbonded parameters is very trivial, since there aren't even any bonded 
parameters to assign, just a single [atoms] directive.  Then just #include it in 
your .top.

-Justin

> [ moleculetype ]
> ; Name            nrexcl
> Other_chain_A       3
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  
> typeB    chargeB      massB
> ; residue   1 GAS rtp GAS  q  0.0
>      1         AR      1    GAS     AR      1          0          1   ; 
> qtot 0
> ; residue   2 GAS rtp GAS  q  0.0
>      2          O      2    GAS     AR      2          0 1.48594e-41   ; 
> qtot 0
> ; residue   3 GAS rtp GAS  q  0.0
>      3          O      3    GAS     AR      3          0 1.48594e-41   ; 
> qtot 0
> ; residue   4 GAS rtp GAS  q  0.0
>      4          O      4    GAS     AR      4          0 1.48594e-41   ; 
> qtot 0
> ; residue   5 GAS rtp GAS  q  0.0
>      5          O      5    GAS     AR      5          0 1.48594e-41   ; 
> qtot 0
> ; residue   6 GAS rtp GAS  q  0.0
>      6          O      6    GAS     AR      6          0 1.48594e-41   ; 
> qtot 0
> ; residue   7 GAS rtp GAS  q  0.0
>  
> 

-- 
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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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