[gmx-users] PBC

Hi, I would like to know if there a way to do an isolated protein simulation (without periodic boundary conditions) and in that case, how can I choose the bondary conditions. I`ve been reading editconf opcion -pbc, and pbc = no in the .mdp files, but it doesn`t seems to work. Hopping to be clear

[gmx-users] RMSD of Aminoacids

Hi, I'm trying to compare two proteins with the same number of aminoacids with g_confrms, and it works all right, but it gives me the RMSD of the hole protein, and I need the distances (or deviations) of each aminoacid. I know this data shoul be there, but I don't know how to get it (I've got the m

[gmx-users] Re: OXY not found

ot; > > > Today's Topics: > > 1. problem in running grompp (victor doss) > 2. problem running grompp - error message here (victor doss) > 3. Re: problem running grompp - error message here > (Justin A. Lemkul) > 4. OXY not found (Andy Torres) > 5. Re:

[gmx-users] OXY not found

Hi, I run pdb2gmx (with all the ff that Gromacs bring by default) on myoglobin (1A6M.pdb) wich I get from the "protein data bank". and I got the following Fatal error: Residue 'OXY' not found in residue topology database I check the ff and I did not found the oxigen molecule. I saw that somebody