Hi everyone
Still waiting for some solution. Any help regarding this would be
appreciated.
Best Regards
On Wed, Feb 15, 2017 at 11:50 AM, ashutosh srivastava
wrote:
> Hi
>
> My system contains protein, ligand (MOL) bound to protein, water(tip3p), 1
> Na and 1 Cl.
> Following
gt; such groups are produced? Please share your terminal output.
>
> Mark
>
> On Wed, Feb 15, 2017 at 1:48 AM ashutosh srivastava
> wrote:
>
> > Hi everyone
> >
> > I have written a python script that takes ligand group name as input and
> > then does som
Hi everyone
I have written a python script that takes ligand group name as input and
then does some analysis. However, the default groups that come out have
repeated instances of ligand name and ions. Upon giving the ligand name as
argument it throws following error.
Error: Multiple groups 'MOL' s
On Mon, Sep 26, 2016 at 11:10 AM, ashutosh srivastava
> wrote:
>
> > Dear Tsjerk
> >
> > Thank you so much for the detailed explanation.
> > So is there a way to extract motions of only ligand, along a particular
> > direction (say rotation along a dihedral
> distorted configuration along the axis.
>
> I hope this clarifies your observations.
>
> Cheers,
>
> Tsjerk
>
> On Mon, Sep 26, 2016 at 4:32 AM, ashutosh srivastava
> wrote:
>
> > Dear all
> >
> > I have performed a 200 ns simulation on a protei
Dear all
I have performed a 200 ns simulation on a protein ligand (MOL) system in
gromacs 5.1.2. Is it possible to get low frequency motions of only the
ligand?
When I am looking at the filtered trajectory (along PC1) after performing
PCA on the protein+MOL the small molecule looks distorted. The
Hi Aswathy
You can make a group with Protein and ligand in an index file using
make_ndx and pass it with -n in gmx rms.
Ashutosh
On Fri, Apr 22, 2016 at 6:46 PM, Aswathy soman
wrote:
> Hi,
> I have done a 100 ns simulation of protein-ligand complex. I was wondering
> is it possible to calculat
