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

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Sep 6 09:43:16 CEST 2005


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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