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Hi Vijay,<br>
<br>
I've CC'd this email to the gmx-users as it's best to keep this on the
list.<br>
<br>
There doesn't seem to be any attached .mdp file with your email.
Maybe it got removed by my mail server. <br>
<br>
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.<br>
<br>
Cheers,<br>
<br>
Bruce<br>
<br>
vijay kumar hinge vijay wrote:
<blockquote
cite="mid:c91230fc0708230248l17f27cf7kea1e7ff61b97151a@mail.gmail.com"
type="cite">hi sir .<br>
thanku for reply <br>
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.<br>
thanking u<br>
bye<br>
vijay kumar <br>
c/o DR.akash ranjan<br>
cdfd<br>
hyderabad<br>
india<br>
<br>
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<br>
<pre class="moz-signature" cols="72">--
"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: <a class="moz-txt-link-abbreviated" href="mailto:bfmilne@ff.up.pt">bfmilne@ff.up.pt</a></pre>
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