Hi,
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.
Cheers,
Bruce
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
CEQUIMED
Faculdade de Farmácia
Universidade do Porto
Rua Aníbal Cunha - 164
4050-047
Porto
Portugal
email: [EMAIL PROTECTED]
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