[gmx-users] water models

Irem Altan irem.altan at duke.edu
Thu Mar 3 23:27:52 CET 2016

> On Mar 3, 2016, at 5:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 3/3/16 2:21 PM, Irem Altan wrote:
>> Hi,
>> 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?
> Normally the water topology is simply taken care of by #including the appropriate stock topology.  pdb2gmx will try to create bonds between the atoms, which is not normal for rigid water models.

So am I incorrect in creating relevant entries in aminoacids.rtp and aminoacids.hdb?

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