Re: [gmx-users] Generating topology for a HEM protein with CHARMM27

2016-05-25 Thread Justin Lemkul
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

Re: [gmx-users] Generating topology for a HEM protein with CHARMM27

2016-05-25 Thread zeineb SI CHAIB
@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

Re: [gmx-users] Generating topology for a HEM protein with CHARMM27

2016-05-24 Thread Justin Lemkul
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

[gmx-users] Generating topology for a HEM protein with CHARMM27

2016-05-23 Thread zeineb SI CHAIB
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

Re: [gmx-users] Generating topology for a hem protein

2016-05-19 Thread Justin Lemkul
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

[gmx-users] Generating topology for a hem protein

2016-05-19 Thread zeineb SI CHAIB
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

Re: [gmx-users] Generating topology for a HEM protein with CHARMM27

2016-05-13 Thread zeineb SI CHAIB
@ 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

[gmx-users] Generating topology for a HEM protein with CHARMM27

2016-05-12 Thread zeineb SI CHAIB
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: