transmembrane protein modeling

Lipid topology (.itp required for GROMACS MD simulations) contains 52 atoms. But lipid bilayer PDB structure consists of (>52)-atom molecules (such a difference is a result of using united-atom force field) with all hydrogens, which were considered in GROMOS96 53a6 FF. It was obtained 52-atom molecules system with:

cat lipid.pdb | grep -v "0.00 H" > lipid-noH.pdb

Output PDB format details depends on software:

mdrun -deffnm box-min -c box-min.pdb -v -nice 0 # output is box-min.pdb [box-min.tpr assumed to be exist]

mdrun -deffnm box-min -c box-min.gro -v -nice 0 # output is box-min.gro

vmd box-min.gro # box-min.gro was converted to box-min(from_gro).pdb with vmd

spdbv box-min.pdb # warning 1: at least one HETATM group lacked proper CONNECT informations. Connection will be generated between atoms that are closer than 2.000A, which can generate false bonds. [CONNECT section was removed manually] warning 2: File ignored (either or is not a valid PDB file, or it contains only a Carbon Alpha trace). => spdbv doesn`t understand GROMACS PDB output

spdbv box-min(from_gro).pdb #warning 1: the same; => successfully opened