Dear People,
I want to study and characterize cavity of a protein. I mean i want to
characterize opening and closing of protein cavity.
Is there any tool of gromacs which will help me do that?. Are there other
softwares to do that?
Thanks
Bhupendra
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* Please
>
> Kevin
>
> On Sat, Mar 31, 2018 at 6:46 AM, Bhupendra Dandekar <
> bhupendra.dandekar...@gmail.com> wrote:
>
> > Hi Gromacs users
> > I wanted to know whether flatbottom restraint does have GPU support or
> > not?.
> >
> > I was trying a
Hi Gromacs users
I wanted to know whether flatbottom restraint does have GPU support or
not?.
I was trying a simulation with gromacs 5.0.6 and gromacs 5.1.4 with gpu in
presence of flatbottom restraints.
But in presence of gpu mode, these give segmentation fault.
But if I run the same program
Dear Farial,
Use this command to install acpype and antechamber using conda:
conda install -c acpype -c openbabel -c ambermd
and then you can check and call acpype, antechamber like this from your
terminal:
acpype -h
antechamber -h
then you can generate ligand topology using this command:
t;
> Alan
>
> On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar <
> bhupendra.dandekar...@gmail.com> wrote:
>
> > Dear Farial,
> >
> > Use this command to install acpype and antechamber using conda:
> >
> > conda install -c acpype -c openbabel -c ambermd
I actually got lot of help from Luciano Kagami about installation and usage
of acpype and ligro.
Thanks to both of you.
Bhupendra
On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar <
bhupendra.dandekar...@gmail.com> wrote:
> Thanks to you also sir.
> Your work is really
ext/plain; charset="UTF-8"
> >
> > We are working on it now. I can't tell you exactly because we need
> several
> > tests. It's a complete new version re-written from scratch.
> >
> > I'm really sorry for the inconvenience but we hope to b
; Today's Topics:
> >
> >1. Error of CgenFF convert to itp (Mijiddorj B)
> >2. acpype and conda (Farial Tavakoli)
> >3. Re: acpype and conda (Bhupendra Dandekar)
> >4. Place a gap in y-axis (Raag S
Hi Farial,
Are you online now?
Bhupendra
On Mon, Oct 29, 2018 at 12:10 PM Farial Tavakoli
wrote:
> Dear Bhupendra
>
> Thanks for your reply
>
> I am in /Downloads/acpype-master/acpype/scripts path and type only acpype
> -h or acpype.py -h , but face with this error:
> acpype: command not
Dear all,
I want to perform LIE calculations. I want to know what are the steps for
LIE calculations.
I know that we need to perform two simulations for Protein-Ligand and
Ligand separately.
Are these two simulations are same as we do in regular MD simulations with
EM->NVT->NPT->Prod-RUN steps?
Dear all,
I want to perform LIE calculations. I want to know what are the steps for
LIE calculations.
I know that we need to perform two simulations for Protein-Ligand and
Ligand separately.
Are these two simulations are same as we do in regular MD simulations with
EM->NVT->NPT->Prod-RUN steps?
I will look into this and get back to you again. But meanwhile just try
using .tpr file instead of.gro file in your pbc correction step.
Thanks
Bhupendra
On Thu, Jan 16, 2020, 10:07 PM Rabeta Yeasmin
wrote:
> Hi Bhupendra,
>
> Thanks for your reply. The RMSD is actually 3.5nm means 35A, which
Dear Rebeta
Did you visualise your trajectory? If not then kindly first do that.
If the protein in your CG simulation is fluctuating a lot then the rmsd of
3.5 can make sense.
Also, prepare a separate index for protein BB(backbone) bead only and use
it in rmsd fitting as well as rmsd
the RMSD after this, it looks reasonable now.
> Thanks for suggesting to check the trajectory.
>
> Rabeta Yeasmin
>
> On Thu, Jan 16, 2020 at 10:46 AM Bhupendra Dandekar <
> bhupendra.dandekar...@gmail.com> wrote:
>
>> I will look into this and get back to you ag
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