[gmx-users] Add custom residue to DNA index group

[william Stebbeds]

Thanks for the quick reply, 

I have already done that, and GROMACS, in all other cases, knows it is DNA, as it automatically forms the bonds with other residues.

it is only when it makes its index files that it doesnt know that my residue is DNA.

Cheers

Will

 




Date: Sat, 12 Feb 2011 03:33:15 +1100
From: Mark.Abraham at anu.edu.au
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Add custom residue to DNA index group



  


    
    Message body
  
  
    On 12/02/2011 3:14 AM, william Stebbeds wrote:
    
      
      Hi Folks,

      

      I have added a custom DNA residue to the amber99sb ff, and
      everything works perfectly, (thanks to Justin!).

      

      The residue is incorporated perfectly into the sequence, with no
      abnormal events during simulations. I have updated all the files
      to include the new residue.

      

      I have since realised, when using g_rms, that my custom residue is
      not included in the default DNA index group, and appears as a
      group on its own.

      

      Is  there a way of making gromacs understand that this residue is
      DNA when it makes the index files?

      

      I am not using make_ndx, I just let gromacs split the groups.

      

      Thanks in advance

      

      Will - Cranfield University

    
    

    You need to arrange for the tools to access a modified form of
    share/gromacs/top/residuetypes.dat with your custom residue suitably
    classified. I understand you can copy that file to your working
    directory and modify it there, and GROMACS will use the local copy.

    

    Mark

  


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