[gmx-users] REMD of IDPs

[João Henriques]

​Dear Yanhua,

To my knowledge (prior to gromacs 5.X at least), there​ are no gromacs
tools able to turn a sequence into a PDB. The user must take care of that
pre-processing on his/her own. I work with IDPs quite a lot, so what I can
tell you is what I usually do. I take my fasta sequence and use PyMOL to
construct the PDB. Then I'm able to feed the PDB to pdb2gmx.

*I'm sure there are a million different ways of doing this, given that
there are so many different protein modelling tools out there.*

Here's one example using Histatin 5.

- On PyMOL's command line type the following (without the quotation marks):
"for aa in "AKRHHGYKRKFH": cmd._alt(string.lower(aa))"

- This builds a fully stretched Histatin 5 3D model which can be exported
as PDB.

- Make sure to use "-ignh" on pdb2gmx, as the resulting hydrogen atom names
are usually incompatible with the force fields I routinely use.

- It's also a good idea to use "-renum" on pdb2gmx as for some reason PyMOL
exports the PDB with residue numberings starting from no. 2.

Cheers,
João


On Fri, Apr 8, 2016 at 4:14 AM, YanhuaOuyang <15901283893 at 163.com> wrote:

> Hi, I have a sequence of an intrinsically disordered protein, I have no
> idea how to start my REMD with gromacs. e.g. how to convert my sequence
> into a pdb file
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