[gmx-users] pdb2gmx

[Eric Smoll]

Mark,

The discrepancy I describe is not a problem. As you mentioned, pdb2gmx is a
tool intended to process input files with a great deal of noise. This tool
can have its own requirements.

What is troublesome is that these differences lead me to question if
separate simulations with different input methods are making use of the
same parameters and that these parameters are correct.

If you are aware of any sanity checks the user can preform, that would be
most useful.

Best,
Eric

On Wed, Oct 29, 2014 at 10:55 AM, Eric Smoll <ericsmoll at gmail.com> wrote:

> Hi Mark,
>
> Thanks for your help. I am looking for a deeper understanding "residue
> names," "atom names," and how they are used to properly form input for
> grompp.
>
> By experimentation, it appears the pdb2gmx requires unique "atom names"
> within each residue of the .rtp file to properly process .gro/.pdb files.
> Thus, every "atom name" of a residue in the .gro/.pdb file must be unique.
> It this not made clear in the .rtp section of the manual. It also appears
> that the bond directive is required, not optional as shown in the example
> in the .rtp section of the manual.
>
> However, if I build a system using an .itp file and the [ molecules ]
> directive, the requirements are more flexible. Again, I observe that while
> the "atoms names" of the gro and .itp files must match within a given
> residue, they need not be unique. This is not made clear in the manual. It
> seems (I hope) that matching is accomplished by the "nr" field of the
> .top/,itp file and the "atom number" field of the .gro/.pdb file.
>
> Best,
> Eric
>
> On Wed, Oct 29, 2014 at 3:56 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> The .rtp files are used by pdb2gmx in order to recognize residues in the
>> face of what can be massive noise in the input file. It primarily matches
>> names of atoms and residues. It writes a coordinate and topology file
>> whose
>> atom and residue ordering matches each other, and whose atom types will
>> permit parameter lookup from the force field data bases - atom and
>> residues
>> names become fairly (completely? idk) unimportant at this stage. I imagine
>> it is possible to duplicate the same atom name within a residue for use
>> with grompp, but likely there's no tool that generates such input for
>> grompp, because they need unique atom names so they can bring order from
>> chaos. Please check out the instructions and examples in Chapter 5 of the
>> manual.
>>
>> Mark
>>
>>
>> On Wed, Oct 29, 2014 at 1:11 AM, Eric Smoll <ericsmoll at gmail.com> wrote:
>>
>> > Hello Gromacs users,
>> >
>> > I would like to add a molecule as a "residue" in the aminoacids.rtp file
>> > and I have a few questions.
>> >
>> > As far as I understand, a residue in a gro file can multiple atoms with
>> the
>> > same "atom name." What links every atom in this residue to parameters in
>> > the top [ atoms ] directive is the *order.* The gro file "atom names"
>> must
>> > match the top file atoms names but the mapping of parameters is done via
>> > the order, correct? This allows atoms in a residue to have the same
>> "atom
>> > name" but be associated
>> > with a different "atom type," "charge group," etc...
>> >
>> > Does an entry in a residue database (e.g., aminoacids.rtp) work the same
>> > way?
>> > The syntax is shown below.
>> >
>> > [ TEST ]
>> > [ atoms ]
>> > ; atom_name    atom_type    atom_charge    charge_group
>> >
>> > I have to specify the "atom name," force field "atom type," "atom
>> charge,"
>> > and "charge group" for every atom in the "TEST" residue in order. The
>> "atom
>> > name" must match the "atom name" in the input coordinate file but the
>> > mapping is applied by the entry order, correct? I do no need unique
>> "atom
>> > names," correct?
>> >
>> > Best,
>> > Eric
>> > --
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