[gmx-users] Re: RE: GROMACS TUTORIAL

[John Kerrigan]

Jayant,

I think that GROMOS96 uses NA+, but Gromacs forcefield uses Na+.  Anyway,
when grompp parses ions.itp, it is looking only for the ion name which
corresponds to the forcefield you are using.  Therefore, check ions.itp
file.  Within that file, each set of ions will be separated based on
forcefield.  Use the ion name from that file corresponds to the forcefield
you are using.

If you do change the ion name, you will need to change the ion name in top
file, gro file, and mdp file.

Hope this helps.

John


 On Wed, 14 May 2003, Jayant James Jayasundar wrote:

> Dr. John,
> As per ur instructions I have subtracted the SOL by a value of 5 
> and added the last line as below
> 
> [ molecules ]
> ; Compound        #mols
> Protein             1
> SOL             12579
> NA+                 5
> 
> But on execution of the grompp for the MD run ( I am giving and 
> restrained run just directly going for the MD run) I get a error 
> message such as
> 
> Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Excluding 3 bonded neighbours for Protein 1
> turning all bonds into constraints...
> Excluding 1 bonded neighbours for SOL 12579
> turning all bonds into constraints...
> Cleaning up temporary file gromppTunBcQ
> Fatal error: No such moleculetype NA+
> 
> but in the ions.itp, the NA+ is present!!!!!
> DO u have any idea where I might be going wrong and how 2 
> rectify
> 
> Thanking you in advance
> Sincerely
> Jayant James
> 
> 
> On Tue, 13 May 2003 John Kerrigan wrote :
> >
> >
> >
> >The genion program will take the coordinates from your tpr file 
> >and replace
> >x number of solvent molecules by x number of ions (whichever you 
> >choose,
> >either Na+ or Cl-) at random.  In the tutorial, you replace 2 
> >solvent
> >molecules with 2 chloride ions.  Therefore, in order for your 
> >topology file
> >to agree with your new coordinate file (gro), you must correct 
> >for this
> >substitution.  In the [molecules] section, you must subtract two 
> > from the
> >number of solvent molecules (labeled SOL) and you must add a line 
> >for the
> >two new chloride ions using whatever label (e.g. Cl) the gromacs 
> >forcefield
> >prefers for this ion.  In addition you must add an include line 
> >to include
> >"ions.itp" to read in parameters for your ions.
> >
> >-----Original Message-----
> > From: Jayant James Jayasundar 
> >[mailto:jayant_jacques at rediffmail.com]
> >Sent: Monday, May 12, 2003 2:23 PM
> >To: kerrigje at umdnj.edu
> >Subject: GROMACS TUTORIAL
> >
> >
> >Dr. John,
> >I am presently using ur GROMACS tutorial downloaded from
> >www2.umdnj.edu/~kerrigje/pdf_files/fwspidr_tutor.pdf
> >in neutralizing my Model by means of counter ions (Na). I am 
> >not
> >able to understand what u mean in PAGE6 with in the box last
> >paragraph. That "add a line for 2Cl molecules in the 
> >[molecules]
> >section of the end of the file".
> >
> >Do i need to add an empty line or
> >Do I need to type Na     5( the number of counter ions ) in the
> >last line???
> >Please help me
> >Thanking you
> >Sincerely
> >Jayant
> >
> >Jayasundar Jayant James
> >Research scholar
> >Centre for Biotechnology
> >Anna University. Chennai - 600 025.INDIA
> >Ph 2350772(Office), Cell-9841042164,
> >Res 4935864
> >___________________________________________________
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> 
> 
> Jayasundar Jayant James
> Research scholar
> Centre for Biotechnology
> Anna University. Chennai - 600 025.INDIA
> Ph 2350772(Office), Cell-9841042164,
> Res 4935864
> ___________________________________________________
> Get www. mycompany .com and 5 matching email ids.
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