On 5/25/16 9:58 AM, zeineb SI CHAIB wrote:
@Justin,
Thank you very much for your help, I finally fixed the problem but I'm having
another one with grompp (which was expected): The error that I get is:
ERROR 7 [file topol.top, line 41571]:
No default Proper Dih. types
Fatal error:
There
@Justin,
Thank you very much for your help, I finally fixed the problem but I'm having
another one with grompp (which was expected): The error that I get is:
ERROR 7 [file topol.top, line 41571]:
No default Proper Dih. types
Fatal error:
There were 13 errors in input file(s)
I think that
On 5/23/16 5:31 AM, zeineb SI CHAIB wrote:
I'm looking to generate the topology of a HEM protein , I choose CHARMM as a
force field. At the begining, when I run pdb2gmx I had this error about missing
hydrogen's:
WARNING:
atom HA is missing in residue HEM 473 in the pdb file
You
I'm looking to generate the topology of a HEM protein , I choose CHARMM as a
force field. At the begining, when I run pdb2gmx I had this error about missing
hydrogen's:
WARNING:
atom HA is missing in residue HEM 473 in the pdb file
You
might need to add atom HA to the hydrogen database
On 5/19/16 9:41 AM, zeineb SI CHAIB wrote:
Dear all,
I'm desperetly looking for help to generate the topology of my hem protein.
I'm using CHARMM as a force field and apparently PDB2gmx assigns dihedrals
that should not exist and it's complicated to verify everything. Justin
suggested
Dear all,
I'm desperetly looking for help to generate the topology of my hem protein.
I'm using CHARMM as a force field and apparently PDB2gmx assigns
dihedrals that should not exist and it's complicated to verify everything.
Justin suggested using
@ Justin
Dear Justin,
Thank you very much for your orientation and help.
I visited CHARMM-GUI website and I found interesting tutorials for my
HEM-protein but before going further I would like to know if it's feasible to
use CHARMM GUI for my Hem-Protein and include after my substrate
Dear gmx users,
I'm working on simulating a homodimer with its cofactors (hem, THG) and its
substrate with GROMACS.
Since my system is complex, I decided to start first with a monomere taking
only protein residues and the hem group.
When I run pdb2gmx, using CHARMM27 FF, I had this error: