[gmx-users] plzz help

I am doing simulation of membrane protein in lipid bi layer for my college project!. can you please elaborate on the shrinking step that needs to be iterated to get the right protein per lipid area. thanks. -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] (no subject)

I am doing simulation of membrane protein in lipid bilayer for my college project!. After making the complex of protein and lipid bilayer, I was going to the step using genbox to solvate the system. The error that i am now getting is : Fatal error: Not enough memory. Failed to realloc

[gmx-users] (no subject)

i am doing protein in bilipid membrane simulation. while packing the protein in the lipid membrane step, i am getting this error. command : perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Reading. Scaling lipids There are 0 lipids... Illegal division by zero at

[gmx-users] help!!

i am using the tutorial KALP15 in DPPC for my protein in bilipid membrane SIMULATION. i have reached Step Three: Defining the Unit Cell Adding Solvent where i hav to pack the lipids around the protein using InflateGro. how do i start using inflategro? my last step was : to generate this new

[gmx-users] Fatal error: atom C not found in buiding block 19NH2 while combining tdb and rtp

i am stimulting an AMP protein in water. this is the error i get on my first step.. pdb2gmx -f 1PG1_1.pdb -o 1PG1_1_processed.gro -water spce error: Fatal error: atom C not found in buiding block 19NH2 while combining tdb and rtp please HELP!! -- gmx-users mailing list

[gmx-users] em fatal error!

*We are trying to do simulation of lysozyme in water.* step with problem : energy minimization. command given: *[root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr* :-) G R O M A C S (-: Getting the Right