I am running a protein ligand MD simulation in gromacs, when I generate ligand.gro file using this command
gmx_mpi editconf -f bg6_ini.pdb -o BG6.gro it gives following at the end
Read 76 atoms No velocities found
Back Off! I just backed up BG6.gro to ./#BG6.gro.2#
gcq#518: "Never mind, death professor, your structure's fine" (TV on the Radio)
I am not sure what is meant by Read 76 atoms No velocities found? I am new to gromacs. please suggest
hi
gmx editconf converts generic structure format to .gro, .g96 or .pdb. (Gromacs info)
This tool does not have the capacity to parameterize organic structures that are not proteins or nucleic acids, so that what you do is only convert from one format to another. If you want to prepare a topology for this ligand I recommend the use of Antechamber (tool of AmberTools [free for academic]) and acpype to convert from amber format to gromacs. In this way you obtain a structure file (ligand.gro) and a topology file (ligand.top). You can edit the latter to convert it into an itp file (ligand.itp) that you can include in the complex's topology file. For more information, I recommend Dr. Justin Lemkul's tutorial, which is very good
(http://www.mdtutorials.com/gmx/complex/index.html)
Best Wishes
Dear Sadaf Rani ,
You can user PRODRUG server (http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg) for generate topology for you ligand (.itp, .gro). cmx editconf not is good for topology genere.
Hi
I think you are providing the command in wrong format in the first place.
check the format,
gmx editconf -f input.gro/pdb -o output.gro/pdb
For performing protein-ligand simulation you must prepare the topology file of ligands from other servers like PRODRG, SwissParam, topolbuilder, antechamber etc. depending upon the force field you are using.
But, before that do extract the docked pose of ligand from ligand-receptor bound structure by using tools like Chimera, Discovery studio or Maestro in the suitable format.
Then add the position restrains of ligand in the main topology file.
regards
Tanuj
Information for velocities can not be stored in .pdb file format (like in .gro file format) and editconf command does not assign velocities automatically. So, when you generate a topology for bg6 from bg6_ini.pdb, there will be no velocities in the output .gro file. However, I suppose that you still have a pretty good topology for bg6 with no velocities. Especially if you use the CGenFF for generation of CHARMM36 force field for bg6 ;)
I think that in your case, velocities can be generated from a Maxwellian distribution (if requested) by grompp command. Go on and prepare the final .gro file for the complex of bg6 and your protein of interest, define the box and solvate the system. Then use a proper .mdp file for grompp which will define the automatical generation for velocities.
But first decide whether velocities are really so important for your task.
Good luck!
http://manual.gromacs.org/programs/gmx-grompp.html
http://manual.gromacs.org/online/mdp_opt.html#vel
- Badges
- Science topic