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

[Rahul Karyappa]

Dear Sir,

 Thank you for your kind reply. I have one polymer with sidegroup
which contains OH group. Is there any provision in Gromacs where I can
remove the bond between O and H, and add Na+ ion at the H's position,
so that it will be O- and Na+.  If I can do this please tell me
how I can? Thanking you in advance.


Rahul Karyapa

NCL, India

-- Original Message --
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Mon, 05 Sep 2005 09:06:03 +0200
Subject: Re: [gmx-users] problem with Na+ ions....
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.
________________________________________________________________________
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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