Hello Mehdi,
It seems to me you are after a Single Point Energy Calculation. The fact that
you have many means that it will be convenient for you to make a loop that
will do the same thing on each pdb file.
Here is some documentation
http://www.gromacs.org/Documentation/How-tos/Single-Point
Dear Groamcs User,
I am new in using Gromacs.
I would be appreciated if you guide me, how to calculate energy from the
coordinates of PDB file? In fact I have thousands of Pdb files and would
like to calculate energy for each of them using Gromacs. Since the Pdb
files are already minimized, obvio
Hi everyone
When I submit a PEO chain consists of 23 monomers to LigParGen
web-based service to make a topology file, there is no problem. But when I
submit a PEO chain consists of 100 monomers I give an error:
* Found residue ligand OXY
* Unknown error. Please, check the input file. If yo
Dear Sudip,
Thanks for answer. gmx sasa gives data such as area vs time, area vs
residue and area vs atom. But I want to have the number of hydrophobic
interaction between protein and ligand during the trajectory and get those
residues took part in this type of interactions.
Best,
Andrew
--
Grom
Hi Andrew,
1) http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 (follow
the 'g_sas' section)
2) You can use gmx_cluster module to do the cluster analysis. The central
frame of the most populated cluster will be the average structure.
Regards,
Sudip Das
PhD Student
C/o. Prof. S.
Hi all,
I did md simulation of protein-ligand complex using gromacs 5.1.3.
1) How to investigate hydrophobic interactions between protein and ligand
during trajectory? Which tool is appropriate for this aim?
2) How to get an average structure from whole of trajectory?
Best,
Andrew
--
Gromacs U
