Hi Marcelo,
thanks a lot for your help!!
> After doing the 'pdb2gmx', created the cell e filled with solvent, use the
> "make_ndx" to create an index of your system. One of the groups should be
> your residues that you want to freeze. Then, in your .mdp file, use
> 'freezegrps' and 'freezedim' in
After doing the 'pdb2gmx', created the cell e filled with solvent, use the
"make_ndx" to create an index of your system. One of the groups should be
your residues that you want to freeze. Then, in your .mdp file, use
'freezegrps' and 'freezedim' in your recently created group.
Don't forget the -n
On 9/4/12 11:59 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Yes okey. I understood.
But I have another question:
Since I only want to minimize the phosphates which I added to the protein
I want to use the freeze option to make sure that the other residues will
not change.
But how
Yes okey. I understood.
But I have another question:
Since I only want to minimize the phosphates which I added to the protein
I want to use the freeze option to make sure that the other residues will
not change.
But how can I say gromacs that it shell make an exception and do not
freeze the phos
Okey,
Thank you!!
> Only the -ignh flag is wrong, as Justin said.
>
> Keep the rest of the command line.
> --
> Marcelo Depólo
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Su
But the rest of the command was correct?
Since I only want to minimize the phosphates which I added to the protein
I want to use the freeze option to make sure that the other residues will
not change.
But how can I say gromacs that it shell make an exception and do not
freeze the phosphate of the
Only the -ignh flag is wrong, as Justin said.
Keep the rest of the command line.
--
Marcelo Depólo
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before post
On 9/4/12 11:21 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
when I want the program "pdb2gmx" only to create a topology file but not
to change anything at the protein. Not even adding hydrogen atoms to the
protein.
Because my protein already has hydrogen atoms. I only
Hi everybody,
when I want the program "pdb2gmx" only to create a topology file but not
to change anything at the protein. Not even adding hydrogen atoms to the
protein.
Because my protein already has hydrogen atoms. I only added one residue
and I want to minimize this residue now.
Do I have to ca
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