[gmx-users] Re: regarding NA+

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Aug 24 09:43:20 CEST 2007

Hi Vijay,

The name in the structure file (taken from the genion -pname option)
does not relate to your error. If it does not match the name in the
topology, it will merely lead to a warning.

Now, in an attempt to resolve your issue, I've browsed through your
recent mails, but there's no proper reference or description of your
problem whatsoever. Besides that, the way you have written it makes it
hard to read, as Mark pointed out earlier. I recall that these are the
two reasons I've refrained from replying in the first place (proving
Mark's point).

But, if you could give us a proper account of your problem, we might
be able to solve it (or you might be able to solve it yourself, since
dealing with and presenting your problem in a structured way may make
it clearer for you too). So...

1. What force field did you use (I believe it was GROMOS96 34a1, in
which case atom name and molecule name are both NA+)?
2. What do the last 30 lines of the topology file say?
3. What's in your .mdp file?
4. What is grompp complaining about (give the output, in particular
the lines about warnings/errors)?

By the way, did you read the Manual/Wiki/FAQ/Mailing-list to see if
your problem was addressed there?


On 8/24/07, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> I have CC'ed the gmx-users to keep record of this; please keep all
> correspondence on the list so everyone can see.
> You had not mentioned in your first mail that you had used genion, hence why I
> asked.  Maybe you can detail for us the steps you used (all of them, including
> the actual command line entries) so we can better analyze what you've done.
> -Justin
> Quoting vijay kumar hinge vijay <vijaybioinfo2 at gmail.com>:
> > hi
> > thanks for reply ..i have used genion  command and added  NA+ ,and -pname
> > too fortunately there is no error after running the command
> > can tou tel me wat might be the reason for the error
> > thanking u
> > vijay
> > CDFD
> > hyderabad
> > india
> >
> ======================
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://bevanlab.biochem.vt.edu/Pages/Personal/justin/
> ======================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

More information about the gromacs.org_gmx-users mailing list