Thank you very much, Justin, for your valuable feedback.
Regards.
Sadaf
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Dear Gromacs users
I am using amber99sb-ildn.ff force field for protein and I used GAFF for
ligand parameterization.
I tried different options e.g using constraint =all bonds as well as
h-bonds. Reducing the time step to 1 fs but still, I could not solve the
problem and get lincs warning
Hi Nikhil,
Lazaro Andres Monteserin Castanedo (lamonteserincastan...@gmail.com) invited
you to edit the folder " dPCA " on Dropbox.
Lazaro Andres said:
"Dear Dr. Lemkul I used the following protocol to generate the (.xpm)
filesI followed the protocol in gromacs website to do dihedral
Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files:
I followed the protocol in gromacs website to do dihedral Principal
Component Analysis:
1) Created an index file (*dangle.ndx*) with a list of the dihedrals to
analyze from my molecule. I wrote this file in a text editor
Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files:
I followed the protocol in gromacs website to do dihedral Principal
Component Analysis:
1) Created an index file (*dangle.ndx*) with a list of the dihedrals to
analyze from my molecule. I wrote this file in a text editor
Hello all,
I was trying to install GROMACS 2020.2 and encountered a failed test at make
check (#43, mdrun). I pasted what I think is the pertinent snippet below and
the full output is in the link:
https://www.dropbox.com/s/nfq6yojjdslhxur/make_check.log?dl=0
The cmake incovation was: cmake ..
On 5/2/20 12:13 PM, Eugene Radchenko wrote:
Hello,
I wanted to report a bug using the Redmine site.
Unfortunately, even after registering, the option to submit an issue is missing
from the Issues page (where I expected it).
While the “File a new issue” link from the main page to
Hello,
I wanted to report a bug using the Redmine site.
Unfortunately, even after registering, the option to submit an issue is missing
from the Issues page (where I expected it).
While the “File a new issue” link from the main page to
https://redmine.gromacs.org/projects/gromacs/issues/new
Oh thank you so much, I did not know it was a reference value. Given a
range of values might exist in one system I'm guessing minimization would
be the only way to deal with such a situation.
Best, Miro
On Sat, May 2, 2020 at 9:53 PM Justin Lemkul wrote:
>
>
> On 5/2/20 6:54 AM, Miro Astore
On 5/2/20 8:21 AM, Sadaf Rani wrote:
Dear Justin
I want to get the equilibrium value for bond, angle and dihedral restraints
to use in free energy calculation as mentioned in:-
https://pubs.acs.org/doi/abs/10.1021/jacs.6b11467
Looking forward to your kind suggestions, please.
You can
Dear Justin
I want to get the equilibrium value for bond, angle and dihedral restraints
to use in free energy calculation as mentioned in:-
https://pubs.acs.org/doi/abs/10.1021/jacs.6b11467
Looking forward to your kind suggestions, please.
Thanks.
Sadaf
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On 5/2/20 6:54 AM, Miro Astore wrote:
Hi all,
I'm trying to make a protein with a fair few disulfide bridges and I
couldn't get it to work. I chose -ss yes and increased the minimum distance
in specbonds.dat but it doesn't seem to want to let me see all possible
pariings.
specbond.dat does
On 5/1/20 2:41 PM, Sadaf Rani wrote:
Dear Gromacs users
I did 50ns MD simulation of a protein-ligand complex. From this trajectory,
I extracted region of trajectory having stable rmsd and generated an
average structure. I want to run this average structure to get an idea of
setting some
On 5/1/20 9:29 AM, John Whittaker wrote:
Hi Mohamed,
Hello everybody,
In order to solve the PBC at the end I use the command:
*gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol *
followed by:
*gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb*
I want to solve
On 4/30/20 2:07 PM, lazaro monteserin wrote:
Dear Dr. Lemkul I did it. It works. Thank you very much for the advise.
Now I am having issues opening the (.xpm) files generated that contain for
example the gibbs energy landscape on the two first eigenvectors of the
dPCA.
If I use the command
Hi all,
I'm trying to make a protein with a fair few disulfide bridges and I
couldn't get it to work. I chose -ss yes and increased the minimum distance
in specbonds.dat but it doesn't seem to want to let me see all possible
pariings.
Any way I can nudge it in the right direction without
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