you have to derive
> them
> yourself or find suitable parameters for them.
>
> -Justin
>
> > Once Again thank you for helping out a gromacs newbie.
> >
> >
> >
> > > Date: Thu, 3 Feb 2011 20:43:24 -0500
> > > From: jalem...@
ou have to derive them
yourself or find suitable parameters for them.
-Justin
Once Again thank you for helping out a gromacs newbie.
> Date: Thu, 3 Feb 2011 20:43:24 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Adding modified nucl
gromacs newbie.
> Date: Thu, 3 Feb 2011 20:43:24 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield
>
>
>
> william Stebbeds wrote:
> > Thanks for the reply,
> >
> > ffamb
any incorrect spacing will screw up the coordinates.
To clarify, are you missing a bond, as your first message would imply? I can
see how you might be missing bonds; your residue definition doesn't specify a
bond to the next nucleotide (i.e. "O3' +P"), although if it's a 3&
structure goes
through pdb2gmx, the new nucleotide appears on the other side of the
pbc, in a straight line (i.e. without form).
Are you saying the coordinate file you gave to pdb2gmx has your modified
residue at one location, and the coordinate file it output has it at
some other location? (Because
C2 H21N2 H22
N9N7C8O8
N2N1C2N3 nucleic_imp_11
DGO was also added to residuetypes.dat. hdb file was also updated, as was
dna.rtp within amber99sb.ff.
The problem is not a simple missing bond, as when the structure goes through
pdb2gmx, the new nucleotide
william Stebbeds wrote:
Hello,
I am attempting to add 8-oxo-dG (8-Oxo-2'-deoxyguanosine) to the
amber99sb force field. This is a simple modification of the H8 hydrogen
on a guanine to an oxygen atom. I have followed the instructions on the
gromacs site on adding residues.
However the new
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