[gmx-users] Add custom residue to DNA index group
william Stebbeds
willstebbeds at hotmail.com
Fri Feb 11 18:37:07 CET 2011
I made the changes to ../gromacs/top/residuetypes.dat
the Make_ndx output:
0 System : 34023 atoms
1 DNA : 650 atoms
2 DGO : 66 atoms
3 K : 43 atoms
4 CL : 21 atoms
5 Other : 66 atoms
6 DGO : 66 atoms
7 K : 43 atoms
8 CL : 21 atoms
9 Ion : 64 atoms
10 DGO : 66 atoms
11 K : 43 atoms
12 CL : 21 atoms
13 Water : 33243 atoms
14 SOL : 33243 atoms
15 non-Water : 780 atoms
16 Water_and_ions : 33307 atoms
This system consists of a 22 residue DNA molecule, two of which are DGO, each have 33 atoms.
I also do not understand why DGO is repeated three times.
Thanks again
will
> Date: Fri, 11 Feb 2011 12:08:52 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Add custom residue to DNA index group
>
>
>
> william Stebbeds wrote:
> > Indeed I did
> >
> > DGO DNA
> >
>
> Did you make the change system-wide, or in a local directory? If the latter,
> you have to issue all your commands in that same directory or else the default
> residuetypes.dat (in GMXLIB) will be read.
>
> Can you post the make_ndx output (i.e. list of groups)?
>
> -Justin
>
> > Cheers
> >
> > Will
> >
> > > Date: Fri, 11 Feb 2011 17:57:32 +0100
> > > Subject: RE: [gmx-users] Add custom residue to DNA index group
> > > From: dsarath at gwdg.de
> > > To: gmx-users at gromacs.org
> > >
> > > >
> > > > 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
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > 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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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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