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

[Tsjerk Wassenaar]

Hi Rahul,

Apparently, in your structure file the sodium ions are placed before the 
solvent. That means that in the .top file they should also be placed before 
as follows:

[ molecules ]
; Compound #mols
Protein 1
Na 10 
SOL 182 

This section needs to correspond to the structure file.

Hope it helps,

Tsjerk

On 9/6/05, Rahul Karyappa <r.karyappa at ncl.res.in> wrote:
> 
> 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<http://xray.bmc.uu.se/%7Espoel>
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-- 
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciencesand Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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