Hi
As you said I checked my structure for any bad contact, but the close atoms are
part of the protein so I can't delete them to minimize the structure. And water
molecules are not that much close to make bad contact with the atom.
And the atom which errored during minimization it's the atom tha
Hi all,
I am interested in how Gromacs works at the back end but I don't have much
C experience so this might be silly.
I have noticed that one of my systems that includes virtual sites parses
fine through grompp in gromacs 2019.1 and 3 but fails in 2020.1 with a
segmentation fault.
21169 Segment
Hello,
Though I don't know the answer to your question, I can offer a
workaround for the task. I have simulated such C-terminally amidated
peptides in vacuum before and I performed the same analysis using the
Hydrogen bonds plugin in VMD.
Hope this helps.
Cheers,
Sahil
On 2020-04-28 07:20
Hi Miro,
This can be of great help and a wonderful learning experience; at the
same time also an enormous time-sink.
First, you did already do a bunch of very helpful work in trying to find
the latest version, where things still work, have the error be
reproducible on a test system.
If y
Dear Gromacs users
I am facing a problem between different versions of gromacs for gmx
pdb2gmx. I have a protein-ligand system, I did all the necessary steps
mentioned in gromacs manual for adding new residue to force field. When I
run this in gromacs 2019 it gives me a warning as below:-
Fatal err
Hi Shakira and Dr. Lemkul,
Thank you so much for your reply! I ended up using an AMBER force field.
Best,
Wei-Tse
On Mon, Apr 27, 2020 at 7:32 PM Justin Lemkul wrote:
>
>
> On 4/27/20 7:43 PM, shakira shukoor wrote:
> > Hi
> > As far as I know tip3p water model is modelled to use in combination
