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

[Sarath Chandra Dantu]

>
> 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.
>

Did you make the change in residuetypes.dat file.
add your residues XXX as DNA in the residuetypes.dat file

eq: XXX  DNA



Best Wishes,

Sarath
> Cheers
>
> Will
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>
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>
>
> 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
>
>
>
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>     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
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>
>
>     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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