I did not change anything in mdp. I remove surface waters which are making
bad contact to the protein.
On Tue, Sep 11, 2018, 2:30 PM ISHRAT JAHAN wrote:
> Thank u for your instant reply.
> What changes you have done in mdp file to remove core dump error?
>
> On Tue, Sep 11, 2018, 1:26 PM Bratin
Thank u for your instant reply.
What changes you have done in mdp file to remove core dump error?
On Tue, Sep 11, 2018, 1:26 PM Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
wrote:
> Ya
>
> On Tue, Sep 11, 2018, 12:45 PM ISHRAT JAHAN wrote:
>
> > Did your problem of core dumped was solved?
> >
Ya
On Tue, Sep 11, 2018, 12:45 PM ISHRAT JAHAN wrote:
> Did your problem of core dumped was solved?
>
> On Tue, Sep 11, 2018, 12:23 PM Bratin Kumar Das <
> 177cy500.bra...@nitk.edu.in>
> wrote:
>
> > No problem...I did for other proteins also...during NVT ensemble it's
> > concentration will be
Did your problem of core dumped was solved?
On Tue, Sep 11, 2018, 12:23 PM Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
wrote:
> No problem...I did for other proteins also...during NVT ensemble it's
> concentration will be fixed.
>
> On Tue, Sep 11, 2018 at 11:22 AM, ISHRAT JAHAN
> wrote:
>
>
No problem...I did for other proteins also...during NVT ensemble it's
concentration will be fixed.
On Tue, Sep 11, 2018 at 11:22 AM, ISHRAT JAHAN wrote:
> But if i remove the water molecule from protein surface its concentration
> will change
>
> On Tue, Sep 11, 2018, 11:10 AM Bratin Kumar Das
But if i remove the water molecule from protein surface its concentration
will change
On Tue, Sep 11, 2018, 11:10 AM Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
wrote:
> What ever solvent u r using can make badcontact with protein..that's why I
> am suggesting
>
> On Tue, Sep 11, 2018, 10:29
What ever solvent u r using can make badcontact with protein..that's why I
am suggesting
On Tue, Sep 11, 2018, 10:29 AM ISHRAT JAHAN wrote:
> Why should we delete all the water from protein surface. Actually i am
> doing this in simulation in a urea box. How do i remove water from protein
>
Why should we delete all the water from protein surface. Actually i am
doing this in simulation in a urea box. How do i remove water from protein
surface?
On Tue, Sep 11, 2018, 10:19 AM Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
wrote:
> Then I think we need to delete all the waters from
Then I think we need to delete all the waters from protein surface
On Tue, Sep 11, 2018 at 10:06 AM, ISHRAT JAHAN wrote:
> I am getting the same error as u have posted today. Segmentation fault core
> dumped. Although my minimization runs properly.
>
> On Mon, Sep 10, 2018, 6:30 PM Bratin Kumar
I am getting the same error as u have posted today. Segmentation fault core
dumped. Although my minimization runs properly.
On Mon, Sep 10, 2018, 6:30 PM Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
wrote:
> You upload the warning given by mdrun. I think there is a problem with the
> initial
You upload the warning given by mdrun. I think there is a problem with the
initial configuration of your .pdb file. Please upload all the lines
written in your terminal during mdrun operation
On Mon, Sep 10, 2018, 4:13 PM ISHRAT JAHAN wrote:
> Thank u for your reply sir. I have changed the
Thank u for your reply sir. I have changed the -Dflexible to -DPosres but
still gets the same problem.
On Mon, Sep 10, 2018 at 3:24 PM Bratin Kumar Das <
177cy500.bra...@nitk.edu.in> wrote:
> I think you should remove define=-DFLEXIBLE
> and define=-DPOSRES in the .mdp file. Give 1000 force
I think you should remove define=-DFLEXIBLE
and define=-DPOSRES in the .mdp file. Give 1000 force constant. Don't
give large force costant.
On Mon, Sep 10, 2018, 3:14 PM ISHRAT JAHAN wrote:
> Dear all,
> I am trying to do energy minimization of two docked protein. At the energy
> minimization
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