[gmx-users] water models

Irem Altan irem.altan at duke.edu
Thu Mar 3 20:22:05 CET 2016


I have two general questions about TIP5P and GROMACS version 5.1.2. (I am using AMBER99SB).

- Is it normal that TIP5P does not work out of the box? When I do pdb2gmx without modifying force field files, I get an error saying Residue 'HO5' not found in residue topology database . This is really confusing, as there exists a tip5p.gro, tip5p.itp, the LJ parameters exists within ffnonbonded.itp, the atoms are defined in atomtypes.atp, but there is nothing within aminoacids.rtp and aminoacids.hdb. Is it meant to be that way?

- This is a more general water model question: what is the purpose of the #ifndef FLEXIBLE section within TIPXP.itp? (or spc, spce). I understand that the bonds and angles sections define the parameters for the desired bond lengths and angles, along with high force constants to constrain them. I also understand that they are constrained with the SETTLES algorithm, but what does #ifndef FLEXIBLE do?


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