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. <smit...@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-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of João > Henriques <joao.henriques.32...@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 <15901283...@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 > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.