[gmx-users] Is cholesterol model available in Charmm36 ff?

[Mark Abraham]

Correct. Pdb2gmx matches atom names of coordinate files to .rtp entries,
and writes files whose atom ordering matches each other, because that is
what grompp requires. The new ordering need not match that of any of the
inputs to pdb2gmx. If the grompp atom *naming* is mismatched, grompp
informs you - just a warning, I think.

Mark
On Mar 19, 2014 2:47 PM, "davhak" <davhak at gmail.com> wrote:

> It is good to know that pdb2gmx does not care about atoms order within a
> residue when comparing input coordinates and the .rtp file.
>
> Thank you very much for the information.
>
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