gmx insert-molecules cannot write PDB files with PDB input for -f - Redmine #1887
I am preparing mixed solvent boxes. When attempting to write a PDB file
as output from gmx insert-molecules, a fatal error is triggered:
-------------------------------------------------------
Program: gmx insert-molecules, version 2016-dev-20160112-e6bc2ea
Source file: src/gromacs/fileio/pdbio.cpp (line 1075)
Fatal error:
Can only print PDB atom lines as ATOM or HETATM records
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------I reduced the problem down to a very simple case: inserting one water into a box containing another water. Interestingly, inserting one water into an empty box works and the PDB file is written:
gmx insert-molecules -f empty.pdb -ci spc1.pdb -nmol 1 -o spc2.pdbbut if there are other coordinates already present, the command fails.
Doing this:
gmx insert-molecules -f spc1.pdb -ci spc1.pdb -nmol 1 -o spc2.pdbtriggers the fatal error, but writing, e.g. GRO format works fine:
gmx insert-molecules -f spc1.pdb -ci spc1.pdb -nmol 1 -o spc2.gro(from redmine: issue id 1887, created on 2016-01-14 by jalemkul, closed on 2016-02-03)
- Changesets:
- Revision 0f34db65 by Teemu Murtola on 2016-02-01T13:30:03Z:
Handle pdbinfo in AtomsBuilder
This makes gmx solvate and gmx insert-molecules work when both -f and -o
are .pdb files (previously, the pdbinfo got out-of-sync when the atoms
were added/removed).
Centralize the defaults for pdbinfo to atoms.cpp.
Fixes #1887.
Change-Id: Ia7e7d991cc35e701729904b8319c53283479d0b1- Uploads: