Hi Justin and Anirban, I started a membrane simulation with POPC bilayer after a training with the given KALP peptide and DPPC bilayer. I am following both of your tutorials (mainly the Justin's). I have problem at where I generate a .tpr file for a DPPC (POPC here)-only system using grompp.
I see another warning on non-matching number of atoms along with the error that you recommended a safe one. My error is Warning: atom name 3340 in topol_popc.top and popc_128b_H.pdb does not match (C12 - H2) Warning: atom name 3341 in topol_popc.top and popc_128b_H.pdb does not match (C13 - O) Warning: atom name 3342 in topol_popc.top and popc_128b_H.pdb does not match (O14 - H1) Warning: atom name 3343 in topol_popc.top and popc_128b_H.pdb does not match (C15 - H2) Warning: atom name 3344 in topol_popc.top and popc_128b_H.pdb does not match (O16 - O) Warning: atom name 3345 in topol_popc.top and popc_128b_H.pdb does not match (C17 - H1) Warning: atom name 3346 in topol_popc.top and popc_128b_H.pdb does not match (C18 - H2) Warning: atom name 3347 in topol_popc.top and popc_128b_H.pdb does not match (C19 - O) Warning: atom name 3348 in topol_popc.top and popc_128b_H.pdb does not match (C20 - H1) (more than 20 non-matching atom names) WARNING 1 [file topol_popc.top, line 26]: 10708 non-matching atom names atom names from topol_popc.top will be used atom names from popc_128b_H.pdb will be ignored Analysing residue names: There are: 128 Other residues There are: 2460 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 42105.00 Largest charge group radii for Van der Waals: 6.115, 5.932 nm Largest charge group radii for Coulomb: 6.546, 6.115 nm WARNING 2 [file em_st.mdp]: The sum of the two largest charge group radii (12.661407) is larger than rlist (0.900000) Calculating fourier grid dimensions for X Y Z Using a fourier grid of 54x56x48, spacing 0.117 0.117 0.119 Estimate for the relative computational load of the PME mesh part: 0.45 This run will generate roughly 34 Mb of data There were 2 warnings ------------------------------------------------------- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1563 Fatal error: Too many warnings (2), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. Can any one of you help me move from here? Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists