[gmx-users] simulation with ligand at the active site

Hello Users, I have a query regarding simulation with the ligand. In my protein there are two ligands, one of them (coenzyme) is from the crystal data, and other I have docked at the active site, while docking it is showing good interaction with all the active site residues very well. I used GROM

[gmx-users] help regarding simulation

Hello All, I want to know one thing that if MD could be used in my case, i have a protein for which crystal structure is known with a conenzyme bound to it. It is given in literature that related proteins of this family shows large conformational change near the substrate binding region when t

[gmx-users] Re: Running MD on a dimeric protein

Hello,, I am really thankful to Mark, Justin and XAvier for helping me to clear my doubts. Reply by Mark is really explainatory. I got my doubts clear. Regards Note: Forwarded message attached -- Original Message -- From: "onetwo "twoon...@rediffmail.com To: gmx-users@gromacs.o

[gmx-users] Running MD on a dimeric protein

Hello Sir, I am simulating a protein which is a homodimer, when I did pdb2gmx, it generated a topolgy file in which there were two chain topologies for each chain as : ; Include chain topologies #include "topol_A.itp" #include "topol_B.itp" and in Compound section gave ;

[gmx-users] Running MD on a dimeric protein

Hello Sir, I am simulating a protein which is a homodimer, when I did pdb2gmx, it generated a topolgy file in which there were two chain topologies for each chain as : ; Include chain topologies #include "topol_A.itp" #include "topol_B.itp" and in Compound section gave ;

Re: [gmx-users] Help in parametrisation

following website http://ffamber.cnsm.csulb.edu/. Any help ? I am really thankful to you for ur time and patience. Regards 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. > >

Re: [gmx-users] Help in parametrisation

the nonbond_params for ffG43a1nb.itp. For both the other two ligands which contains phosphate and enol groups, I was able to create topology using PRODRG server. Regards onetwo wrote: > Hello All, > > I am new in this field, and I want to do simulation study on one of the > protei

Re: [gmx-users] Help in parametrisation

the nonbond_params for ffG43a1nb.itp. For both the other two ligands which contains phosphate and enol groups, I was able to create topology using PRODRG server. Regards onetwo wrote: > Hello All, > > I am new in this field, and I want to do simulation study on one of the > protei

[gmx-users] Help in parametrisation

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