Re: [gmx-users] mktop

ram bio wrote: Dear Justin, Thanks. The POPC bilayer i am using is with berger lipids, corrected for dihedrals so as to be compatible with the OPLS FF for aminoacids. I think significantly more parameters than just dihedrals need to be altered to make the Berger united-atom force fie

Re: [gmx-users] mktop

Dear Justin, Thanks. The POPC bilayer i am using is with berger lipids, corrected for dihedrals so as to be compatible with the OPLS FF for aminoacids. While searching for the literature on compatibility of lipid FF and protein FF, I found few references where similar modification was done for

Re: [gmx-users] mktop

ram bio wrote: Dear Justin, Thanks, and I accept your suggestions; If SwissParam was designed to be used with CHARMM, the most intuitive next step is to use CHARMM for the MD, is it not?I understand the point about trying to keep the force fields consistent between docking and MD, but it m

Re: [gmx-users] mktop/swissparam

> Thanks, and I accept your suggestions; > > If SwissParam was designed to be used with CHARMM, the most intuitive next > step is to use CHARMM for the MD, is it not?I understand the point about > trying to keep the force fields consistent between docking and MD, but it > may not be feasible (i.e.,

Re: [gmx-users] mktop

Dear Justin, Thanks, and I accept your suggestions; If SwissParam was designed to be used with CHARMM, the most intuitive next step is to use CHARMM for the MD, is it not?I understand the point about trying to keep the force fields consistent between docking and MD, but it may not be feasible (i.

Re: [gmx-users] mktop

ram bio wrote: Dear Justin, As i generated the protein-ligand docked complex using opls FF, for the consistency, i am trying to use opls ff generated ligand parameters during md simulations in lipid bi layer. I found that MKTOP can generate topology files using opls ff for small molecules.

Re: [gmx-users] mktop

Dear Justin, As i generated the protein-ligand docked complex using opls FF, for the consistency, i am trying to use opls ff generated ligand parameters during md simulations in lipid bi layer. I found that MKTOP can generate topology files using opls ff for small molecules. I have also tried s

Re: [gmx-users] mktop

ram bio wrote: Dear Justin, Thanks for the information. Initially, i just wanted to run a simulation of protein-ligand in water solvent . I renamed the topology.top generated from mktop to ligand.itp; and included the ligand.itp line in the topol.top file generated from the pdb2gmx. During

Fwd: [gmx-users] mktop

Dear Justin, Thanks for the information. Initially, i just wanted to run a simulation of protein-ligand in water solvent . I renamed the topology.top generated from mktop to ligand.itp; and included the ligand.itp line in the topol.top file generated from the pdb2gmx. During the pdb2gmx command,

Re: [gmx-users] mktop

ram bio wrote: Dear Gromacs Users, I am using opls FF for my protein-ligand simulations in lipid bilayer. I have generated the topologies for the ligand using MKtop. The output from the MKTOP gives the top file, but not the coordinate/structure file. Please let me know if any tutorial is a

[gmx-users] mktop

Dear Gromacs Users, I am using opls FF for my protein-ligand simulations in lipid bilayer. I have generated the topologies for the ligand using MKtop. The output from the MKTOP gives the top file, but not the coordinate/structure file. Please let me know if any tutorial is available for merging t