[gmx-users] costu, fragment force field

I'm attempting to build a costume fragment library of beta amino acids with GAFF parametrization. I have converted the AMBER assigned parameters with acpype, built my .rtp .atp and .itp files. Everything works fine, until grompp, there i get a lot of "No default Ryckaert-Bell. types" errors. The pr

Re: [gmx-users] dendrimer simulation

Thank you for the fast answer, i will do that then. Do i have to close this thread, or it will fade by itself? Lukacs > > > On 7/24/12 10:14 AM, neme...@pharm.u-szeged.hu wrote: >> I have to simulate a G0 PAMAM dendrimer, functionalized on the 4 hands >> with peptide oligomers. I have succesfully

[gmx-users] dendrimer simulation

I have to simulate a G0 PAMAM dendrimer, functionalized on the 4 hands with peptide oligomers. I have succesfully generated the .itp file needed, and have run some simulation. The same applies to the peptide. However i run into problems combining them. It appears the specbond.dat file is only appli