[gmx-users] Re: error regarding NA+ atom (vijay kumar hinge vijay)

Bruce Milne bfmilne at ff.up.pt
Wed Aug 22 12:23:04 CEST 2007


What force field are you using? It may be that the sodium ion is named 
differently e.g. NA instead of NA+. Check in the force field .atp file 
for the correct name and make sure you use that in your .top file. Maybe 
that's all that's wrong.



> Respected sir/madem,
> i am using gromacs - 3.1.4  version on sunsolaris platform.i got error at
> position restrain at grompp step ,telling dat  NO SUCH MOLECULE TYPE
> NA+(both are in caps).beofre dat the error which i got , ihv done following
> steps
> 1.first i hv excuted pdb2gmx command den i noted down the charge which given
> as out put.charge is -1
> 2.after editconf(-d 0.9),genbox ,energy minimization(grompp,mdrun)  i had
> manipulated da  .top file by adding #include 'ions.itp,removed one water
> molecloe from SOL and added NA+     1 at da end of topology file .
> den i got error after runing da grompp of position restrain ,and i had
> changed pr.mdp file ,in that i was added da SOL,0.1,300 (temp)
> thanking u for ur patiency
> regards
> vijaya kumar hinge
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"Hamewith - the road that's never dreary"

Dr. Bruce F. Milne
Faculdade de Farmácia
Universidade do Porto
Rua Aníbal Cunha - 164

email: bfmilne at ff.up.pt

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