pdb2gmx fails to generate pr-files when no water is present
When I issue the command:
pdb2gmx -f _10naked.pdb -o i -p i -i i -vsite hydrogens -water spce
using the AMBER03-port, no i_[AB]_pr.itp files are generated. Now, if I do the
same thing with _10ns.pdb such files are generated. _10ns.pdb and _10naked.pdb
both contain the same DNA molecule, but _10ns.pdb also contains solvent and
ions. In fact, _10naked.pdb was made by executing "grep -v -e SOL -e Na -e Cl
_10ns.pdb > _10naked.pdb".
This problem arises under gmx 3.3.2b and 4.0. I'll provide the relevant files.
#4 Updated by Erik Marklund over 12 years ago
It seems that the pr-block is present after all. In the case of the naked DNA
the pr-block was synonymous with the file i.itp, #included from i.top. When
solvent was present in the pdb-file i_[AB]_pr.itp contained the pr-block and was
#included from i.itp. I just got confused by this inconsistency, or whatever you
may want to call it.