Re: Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

Hi Justin, Thanks a lot for the replies. I wonder what are the newer versions you indicated, but I find one as: *A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and

Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

Yun Shi wrote: Hi Justin, Thanks a lot for the replies. I wonder what are the newer versions you indicated, but I find one as: /A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers,

Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

Thanks again. Since I am running MD simulation on a public cluster, I cannot modify atomtypes.atp and ffnonbonded.itp on that cluster. But I could get every parameter ready and prepare the xxx.tpr files locally, and pass them to the cluster. So the practical question is, does the tpr file

Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

Yun Shi wrote: Thanks again. Since I am running MD simulation on a public cluster, I cannot modify atomtypes.atp and ffnonbonded.itp on that cluster. You can make local copies in your working directory and call that force field when running grompp. But I could get every parameter

[gmx-users] charge assignment for the anomeric carbon in 53a6 ff

Hi all, I am doing MD simulation of some carbohydrate-protein complex with this 53a6 force-field. I noted that in any oligosaccharide, the charge assigned for anomeric carbon is 0.232 while C5 (i.e. in a non-terminal mannopyranose) is 0.376. This is kind of counter-intuitive for me since the

Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

Yun Shi wrote: Hi all, I am doing MD simulation of some carbohydrate-protein complex with this 53a6 force-field. I noted that in any oligosaccharide, the charge assigned for anomeric carbon is 0.232 while C5 (i.e. in a non-terminal mannopyranose) is 0.376. This is kind of

[gmx-users] Charge assignment

Hi everyone.   I'm working on getting parameters for a protein system that has some linker residues in it.  These linkers are nothing too strange, they just have some amine groups.  I can get bonded parameters from the prodrg server.  I know the charge groups are unreliable.  I'm using the 53A6

Re: [gmx-users] Charge assignment

Michael McGovern wrote: Hi everyone. I'm working on getting parameters for a protein system that has some linker residues in it. These linkers are nothing too strange, they just have some amine groups. I can get bonded parameters from the prodrg server. I know the charge groups are