[gmx-users] Where to add Na+ ions data

[Rahul Karyappa]

Respected Sir,

    I am generating my structure (.pdb) using Cerius2
software. There I am putting my model in the box and performing energy
minimization.  As you told I first removed Na+ ions from the .pdb
file. Then I generated .gro and .top files using PRODRG website. Then I
added Na+ ions again in the .gro file. But my question is where to add
Na+ ions in the .top file? In the beginning of the file I added
#include "ions.itp" and in the last like this:

[ system ]

; Name

Protein


[ molecules ]

; Compound        #mols

Protein             1

SOL               182

Na                 10

But after this when I ran grompp it gave me following errors:

processing coordinates...

Warning: atom names in topol.top and out1.gro don't match (OW - NAA)

Warning: atom names in topol.top and out1.gro don't match (HW1 - NAB)

Warning: atom names in topol.top and out1.gro don't match (HW2 - NAC)

Warning: atom names in topol.top and out1.gro don't match (OW - NAD)

......


And when I ran mdrun it gave me following errors:


Back Off! I just backed up step5.pdb to ./#step5.pdb.1#

Wrote pdb files with previous and current coordinates

Warning: 1-4 interaction between 15 and 20 at distance larger than 1 nm

These are ignored for the rest of the simulation

turn on -debug for more information


Back Off! I just backed up step6.pdb to ./#step6.pdb.1#

Wrote pdb files with previous and current coordinates


Back Off! I just backed up step7.pdb to ./#step7.pdb.1#

Wrote pdb files with previous and current coordinates


Where am I going wrong? Is it correct? Or I need to add them where we specify other atoms in the .top file.

waiting for your kind reply.

Rahul Karyappa

NCL, Pune

-- 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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