[gmx-users] REMD of IDPs

[Smith, Micholas D.]

Very good point from João. Always remember to check that your box length is big enough!

===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of João Henriques <joao.henriques.32353 at gmail.com>
Sent: Friday, April 08, 2016 8:24 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] REMD of IDPs

One small remark to Micholas' email​:

- Make sure the simulation box is big enough to allow the IDP to fully
stretch without interacting with its periodic image(s). This is non-trivial
if you build your system from a random coil. That's why I start from a
fully stretched conformation instead of a more representative conformation
of the system. Much easier to control and the time it takes to get to a
"meaningful" conformation is minimal.

/J



On Fri, Apr 8, 2016 at 2:10 PM, Smith, Micholas D. <smithmd at ornl.gov> wrote:

> Dear Yanhua,
>
> Converting a sequence into a structure is itself an "open" problem in
> computational biology/biophysics. There are ways to generate potential
> structures if you also happen to have some restraints from NMR or other
> experiments (small-angle scattering or CD-Spectra) noted in the literature,
> but getting to the "native" fold is very challenging. One program that
> tries to address the sequence to structure problem is Rosetta (
> http://robetta.bakerlab.org/ ).
>
> If you have a short IDP fragment (less than 20 residues), one thing you
> can do it use something like Schrodinger's Maestro program (its free from
> their webpage www.schrodinger.com) and use the molecule builder to "grow"
> the chain as a random coil (random phi-psi placement), save the PDB from it
> and then run MD at high temp to relax the structure into a potential
> starting structure. If it is longer, the IDP may have small structural
> segments (the chain is dominated by disorder but may have short-lived,
> meta-stable, secondary structure regions) in which case you can either try
> to build the molecule with a corresponding secondary structure distribution
> (using Maestro) or try using Rosetta and refine with energy minimization.
>
> Good Luck!
>
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of João
> Henriques <joao.henriques.32353 at gmail.com>
> Sent: Friday, April 08, 2016 3:51 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] REMD of IDPs
>
> ​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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