[gmx-users] problem with Na+ ions....

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 5 09:06:03 CEST 2005

On Mon, 2005-09-05 at 11:41 +0530, Rahul Karyappa wrote:
> Dear all,
>     I have structure with defined Na ions in it. I have a .pdb file of
> that structure and I want to convert it to .gro and .top files. When I
> tried it on PRODRG website it gave me error that Na+ is not supported.
> Then I defined all the atoms in .rtp file also Na. But it's not
> working. What can I do for this? I have included "ions.itp" file in
> the .top file. Do I need to delete the Na+ entry in the .top file. I
> can't delete them from .gro file because their coordinates are
> specified. What Should I do?
take out Na from your pdb file, make the topology and add the Na back in
manually. check chap. 5 in the manual.
> Thanking you in advance.
> Rahul Karyappa
> NCL, India
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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