genbox mixes residue names for mixed solvent box
I have copied a urea + water box urea+h2o.gro from an older distribution of GROMACS and am trying to solvate a peptide with it. Either solvating a peptide or just replicating the box produces a coordinate file
with misnamed residues. Here is a sample command:
~/prog/gromacs-4.5.1/bin/genbox -cs urea+h2o -box 3 3 3 -o urea+h2o333
the urea+h2o333.gro file looks OK on graphics, but the residue names are mixed - some urea molecules
are named 'SOL' and some water molecules are named 'URE'. Also, when solvating the peptide, the
.top file only shows that 680 SOL molecules were added, not how many URE and SOL ...
I attach the input urea+h2o.gro coordinate file