On 3/9/19 4:54 PM, alex rayevsky wrote:
Dear Users and masters!
I know that gromacs can prepare the topology with covalent bonding of
cys-cys bridges in the individual chain on fly. However, when two different
chains are connected with such bonds and the intital geometry is
satisfactory
On 3/9/19 12:23 PM, Stefano Guglielmo wrote:
Dear gromacs users,
I have a system with a topology generated from Amber and then converted
through ParmEd into gromacs-formatted stuff. I would like to add distance
restraints for several pairs of atoms (ca 20). Is it possible to add them
with
Dear Users and masters!
I know that gromacs can prepare the topology with covalent bonding of
cys-cys bridges in the individual chain on fly. However, when two different
chains are connected with such bonds and the intital geometry is
satisfactory (distance, angle) It doesn't work. It was done
Dear gromacs users,
I have a system with a topology generated from Amber and then converted
through ParmEd into gromacs-formatted stuff. I would like to add distance
restraints for several pairs of atoms (ca 20). Is it possible to add them
with grompp or should I edit the .top file some way?
Hi,
The gmx pairdist tool has a lot of capabilities that look like you can
already do exactly what you want, either with multiple selections or well
chosen grouping within selections. Do check the docs.
Mark
On Sat., 9 Mar. 2019, 15:00 Pandya, Akash,
wrote:
> Hi all,
>
>
> My protein is 168
Hi all,
My protein is 168 amino acid residues long. I want to calculate the pairwise
distance between the COM of each individual residue and my ligand molecules
during my trajectory. As I have 168 amino acids, this will take ages if I run
the gmx pairdist code each time. I was wondering
Hello Dear All
I did a simulation of protein-protein interaction. I want to obtain a
distance residue between the two proteins. In the Gromacs tutorial has been
said to calculate of distance for protein-ligand whereas I want to
calculate of distance for protein-protein.
The command of
