[gmx-users] Re: regarding NA+atom type

Bruce Milne bfmilne at ff.up.pt
Thu Aug 23 12:31:56 CEST 2007

Hi Vijay,

I've CC'd this email to the gmx-users as it's best to keep this on the list.

There doesn't seem to be any attached .mdp file with your email. Maybe 
it got removed by my mail server.

If you are using ffG43a1 (Gromos96) then the sodium name should be NA+ 
with the charge included just as you were using at the start. So, maybe 
grompp is complaining because it doesn't find the atom type in the 
actual coordinate (.gro) file although it is defined in the topology. 
Maybe you changed the .top file but didn't make the matching change in 
the .gro file. You would also have to delete a water molecule in the 
.gro file and then add your sodium in the position of the deleted water 
so that it matches the .top description. You can do this by hand but 
probably the best way is to use the genion program to do it automatically.



vijay kumar hinge vijay wrote:
> hi sir .
> thanku for reply
> i have searched  for the file for force field .atp in my 
> GROMACS(3.2.0) .but i haven't got any file like that and i had used 
> force field 2(4a1,official).even i checked for the  all  the possibles 
> of NA(NA+,NA,Na,na).fortunately my gromacs simulation running by 
> changing the my pr.mdp file i think dere might be mistake it my pr.mdp 
> file plz can u tel wat might be the reason for this error.i compared 
> two pr .mdp files (old,new) came to know that some of the parameters 
> are not specified stil im unable find clear error couse.
> thanking u
> bye
> vijay kumar
> c/o DR.akash ranjan
> cdfd
> hyderabad
> india
> -- 
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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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