Dear users, I'm trying to create a box with a number (64) of small peptide molecules (diphenylalanine) solved in ethanol for a Gromacs run with the Martini coarse-grain force field. I've created the box with the solute with the genbox -ci command: genbox -ci FFMM_cg.pdb -nmol 64 -box 5 5 5 -o FFMM_box.gro. This all seemed to work fine and I confirmed that it worked in VMD.
However, when I try to fill the box with ethanol, this gives problems: genbox -cp FFMM_box.gro -cs ethanol_cg.pdb gets stuck at "Reading solvent configuration "" solvent configuration contains 1 atoms in 1 residues" (no error message, but just stops). 1 atom in 1 residue is correct for my pdb file, since ethanol is represented by 1 atom in Martini. I have tried to circumvent this problem by using the ci option again to add ethanol molecules 1 by 1. This kind of works, but if I try it for too many molecules (nmol >15000) it crashes as well with the message 'killed'. Also solving in ethanol that's not converted to coarse grain gets stuck (except from that it says 9 atoms in 1 residue). I have tried to solve it in the spc216 water, this works, so there must be something wrong with my pdb file for the solvent. I can see in other solvent gro/pdb files that there are usually a lot of solvent molecules in 1 file. Why is that and what can I do to make the ethanol box? Thanks very much in advance, Pim PhD student University of Strathclyde Pure & Applied Chemistry / Biomolecular and Chemical Physics -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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
