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.
Cheers,
Bruce
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
--
This message has been scanned for viruses and
dangerous content by *MailScanner* <http://www.mailscanner.info/>, and is
believed to be clean.
------------------------------------------------------------------------
No virus found in this incoming message.
Checked by AVG Free Edition.
Version: 7.5.484 / Virus Database: 269.12.2/967 - Release Date: 22/08/2007 18:51
--
"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]
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
