onetwo wrote:
Hello Justin,
Thanks for the reply.
Sorry to say but I chose the GROMOS force field as for that topology of
the ligands could be prepared by PRODRG and I followed tutorials
available for Gromacs and most of them used GROMOS forcefield and for
starting, parameters used in the t
Hello Justin,
Thanks for the reply.
Sorry to say but I chose the GROMOS force field as for that topology of the
ligands could be prepared by PRODRG and I followed tutorials available for
Gromacs and most of them used GROMOS forcefield and for starting, parameters
used in the tutorials helped me
onetwo wrote:
Thanks Justin for the help,
I have Manganese in my protein with other two ligands at the active site.
I am using GROMOS96 43a1 force field.
Mangnese may have topology similar to Magnesium 2+, What I found is that
Assuming a transition metal "may" be similar to another species
Thanks Justin for the help,
I have Manganese in my protein with other two ligands at the active site.
I am using GROMOS96 43a1 force field.
Mangnese may have topology similar to Magnesium 2+, What I found is that I need
to do changes in ffG43a1.rtp and ffG43a1nb.itp. But how should I calculate
Thanks Justin for the help,
I have Manganese in my protein with other two ligands at the active site.
I am using GROMOS96 43a1 force field.
Mangnese may have topology similar to Magnesium 2+, What I found is that I need
to do changes in ffG43a1.rtp and ffG43a1nb.itp. But how should I calculate
onetwo wrote:
Hello All,
I am new in this field, and I want to do simulation study on one of the
protein conatining a metal ion and study its ability to form
co-oridnation bond with other ligand, which is not defined in GROMOS
force field which I have tried. If this choice of force field is
Hello All,
I am new in this field, and I want to do simulation study on one of the protein
conatining a metal ion and study its ability to form co-oridnation bond with
other ligand, which is not defined in GROMOS force field which I have tried. If
this choice of force field is correct for such
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