Hello, I have been running a simple simulation where I replace 150 water molecules in a waterbox with a lipid called DPC to create micelles. This simulation is working fine and I'm getting decent micelles fairly quickly. I am now trying to do the same, but with a small peptide in the simulation box. I think that grompp is using water molecules coordinates to locate the DPC, making non-sensical molecules. Why is grompp doing this in the simulation with the peptide and not without is what stomps me. Here follow more details about my system and errors:
A PDB of this atomic mess can be found here: http://www.cs.dal.ca/~cblouin/gromacs/gromppout.pdb I've been working on this for a while now, with no success. Can anyone point me in the right direction? Thanks, Christian -------------------------------------------------- Here are the command lines that I use: pdb2gmx -f 2LOU.pdb -o protein.gro -i ./include.itp -p protein.top -ignh editconf -f protein.gro -o protein-PBC.gro -bt dodecahedron -d 1.0 genbox -cp protein-PBC.gro -cs spc216.gro -ci dpc -nmol 150 -p protein.top -o protein-water.gro python edittop.py (this python script adjust the protein.top file for the right count of DPC and adds the include statement for DPC). grompp -f minim.mdp -c protein-water.gro -p protein.top -o protein-water.tpr -maxwarn 4 The last grompp command generates the following warning: Warning: atom name 665 in protein.top and protein-water.gro does not match (OW - C1) Warning: atom name 666 in protein.top and protein-water.gro does not match (HW1 - C2) Warning: atom name 667 in protein.top and protein-water.gro does not match (HW2 - C3) ... WARNING 1 [file protein.top, line 4194]: 6900 non-matching atom names atom names from protein.top will be used atom names from protein-water.gro will be ignored If I extract a PDB from the tpr file, the system looks fine except for all of the DPC atoms are now crammed into a rectangular box at the edge of my PBC. In fact, it looks like the coordinates used for the DPC molecules are these of water molecules that got reassigned to the lipids residues. The topology and gro file (if this helps): http://www.cs.dal.ca/~cblouin/gromacs/protein.top http://www.cs.dal.ca/~cblouin/gromacs/protein-water.gro -- 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