[gmx-users] ATB topology: itp to top conversion

[Anna Lappala]

Dear all,

I am confused: I have my pdb file as well as the itp file produced by ATB. I want to convert these into top and gro files but the molecule is not recognised by the forcefield when I do the following:

pdb2gmx -f input.pdb -o output.gro -i topology.itp 

I have looked through tutorials and on the mailing list, but mostly the workaround is to #include the itp file into an existing top file - which i do not have because i only have a heteromolecule, and no protein...

Many thanks for any suggestions.
Anna