[gmx-users] error regarding NA+ atom

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 22 12:41:35 CEST 2007

Quoting vijay kumar hinge vijay <vijaybioinfo2 at gmail.com>:

> 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 .

Did you use genion to actually add an NA+ ion?

> 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


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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