[gmx-users] genion -pname no NA molecule (sodium) type

Wholly Peach whollypeach at yahoo.com
Sat Mar 17 06:57:46 CET 2012

Will you please tell me where can I find the ions.itp file?
I am looking forward to getting your reply.

 From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, 17 March 2012 3:55 PM
Subject: Re: [gmx-users] genion -pname no NA molecule (sodium) type

On 17/03/2012 4:48 PM, Wholly Peach wrote: 

>Dear All,  
>I use the following to neutralize the charge  
>"genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8",  
>Then I do the following "grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr"".  
>However the feedback says there is no Na (sodium) moleculetype. 
Your force field defines [moleculetype] sections for ions in its
      ions.itp file. Go and look at it, compare with your .top and see
      what the problem is. Atom names, residue names and moleculetype
      names are all different things, and each part of your .top must
      match the right name at the right time.

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