[gmx-users] Reconstruction of atomistic details from coarse-grained-structures

Thu Mar 17 18:15:07 CET 2016

Hi James,

Yes, that is possible too. If you need a hand, contact me off-list.

Best,

Tsjerk
On Mar 17, 2016 16:32, "James Starlight" <jmsstarlight at gmail.com> wrote:

> btwh dont understand clearly the whole methodology
>
> for instance If I have coarse'grained system obtained from the
> martinize tool consisted of the 1) many proteins embedded within big
> bilayer and at the same time 2) FG full atomistic topology for one
> protein (without lipids etc) parametrized via ff wich I am going to
> use in subsequent CG to FG conversion- will it be sufficiant for the
> succesfull FG- CG- FG conversions of the protein7 So will it be
> possible to extract CG protein firstly from the whole CG system via
> editconf and that obtain its FG representation using ./initram.sh?
>
> Thanks!!
>
> 2016-03-17 17:26 GMT+01:00 James Starlight <jmsstarlight at gmail.com>:
> > Yep thanks you are right!
> >
> > It seems that lacking of the FG topology is real problem here.
> > Does the |Reverse transformation| method also require the same input
> > data for back to FG representation including innitial FG topology7
> >
> > Thanks in advance!
> >
> > J.
> >
> > 2016-03-17 17:20 GMT+01:00  <carlos.navarro87 at gmail.com>:
> >> Hi James,
> >> From the tutorial I sent you:
> >> To run the script we need the following:
> >>
> >> The CG structure to backmapp, provided in CG_posre.gro - The CG
> structure you want to back map.
> >>
> >> A complete fine-grained force field corresponding to all the CG
> molecules in CG_posre.gro. Here we use CHARMM36, see all .itp files
> provided and topol.top, which contains the molecules in the same order they
> are present in CG_posre.gro and with the same names. Note, water and ions
> can be skipped in the .top files as they are automatically detected by
> backward.py. - An AA topology of your system (*itp and *top files in an AA
> representation).
> >>
> >> A .map file in the Mapping directory for all residues and molecules to
> be backmapped (water and ions can also be skipped here as their definitions
> are included in backward.py). - A mapping file that will be use to
> reconstruct your CG structure to a FG one based on the topology.
> >>
> >> According to this, is not posible to reconstruct your system without
> the FG topology.
> >>
> >>
> >> --
> >>
> >> Carlos Navarro Retamal
> >> Ingeniero en Bioinformática
> >> Ph. D (c) en Ciencias Aplicadas.
> >> Centro de Bioinformática y Simulación Molecular
> >> Universidad de Talca
> >> Av. Lircay S/N, Talca, Chile
> >> T: (+56) 712201 798
> >> E: carlos.navarro87 at gmail.com o cnavarro at utalca.cl
> >>
> >> On March 17, 2016 at 1:12:47 PM, James Starlight (
> jmsstarlight at gmail.com) wrote:
> >>
> >> what I have found from the
> >> ./initram.sh -h
> >>
> >> -f Input coarse grained structure
> >> *FILE: None
> >> -p Input atomistic target topology
> >> *FILE: None
> >>
> >>
> >> does it means that -p should be full atomic topology of the system
> >> (not coarse grained) ? Is so whether is possible to make such CG to FG
> >> conversion having only CG input data
> >>
> >> 2016-03-17 17:04 GMT+01:00 James Starlight <jmsstarlight at gmail.com>:
> >>> Just tested the ./initram.sh script embedded within the
> >>>
> >>> Unfortunatelly for my case It didnt works
> >>>
> >>> 1- I firstly extract the gro file consisted of the protein CG
> >>> representation only from my Cg.gro using below command and selecting
> >>> protein group
> >>> g_editconf -f system.gro -n -o protein.gro
> >>>
> >>> than I edit my topology putting here only protein itp
> >>>
> >>> #include "./params/martini_v2.1.itp"
> >>> #include "./params/D2.itp"
> >>>
> >>> [ system ]
> >>> Single Low D2
> >>>
> >>> [ molecules ]
> >>> D2 1
> >>>
> >>>
> >>> finally than I apply script on those two files
> >>> ./initram.sh -f protein.gro -o aa_charmm.gro -to charmm36 -p
> protein.top
> >>>
> >>>
> >>> obtaining error
> >>>
> >>> -------------------------------------------------------
> >>> Program g_grompp, VERSION 4.5.7
> >>> Source code file:
> >>> /builddir/build/BUILD/gromacs-4.5.7/src/kernel/grompp.c, line: 523
> >>>
> >>> Fatal error:
> >>> number of coordinates in coordinate file (0-backward.gro, 0)
> >>> does not match topology (backmapped.top, 598)
> >>> For more information and tips for troubleshooting, please check the
> GROMACS
> >>> website at http://www.gromacs.org/Documentation/Errors
> >>> -------------------------------------------------------
> >>>
> >>> 2016-03-17 16:24 GMT+01:00 James Starlight <jmsstarlight at gmail.com>:
> >>>> Is it better than
> >>>>
> http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Reverse-transformation
> >>>> 7 PArticularly for my case I need to convert from CG to FG the
> >>>> structure of GPCR simulated within CG lipids excluding lipids in the
> >>>> final FG model.
> >>>>
> >>>> 2016-03-17 15:49 GMT+01:00 <carlos.navarro87 at gmail.com>:
> >>>>> Hi James,
> >>>>> There is a nice method (developed by Dr. Tsjerk A. Wassenaar) to
> reconstruct the atomistic structure from a CG structure.
> >>>>> Here is the respective tutorial
> http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Backward
> (from the MARTINI group), and here is the paper of the back mapping method:
> >>>>> http://pubs.acs.org/doi/abs/10.1021/ct400617g
> >>>>> Hope this helps.
> >>>>> Best,
> >>>>> Carlos
> >>>>> --
> >>>>>
> >>>>> Carlos Navarro Retamal
> >>>>> Ingeniero en Bioinformática
> >>>>> Ph. D (c) en Ciencias Aplicadas.
> >>>>> Centro de Bioinformática y Simulación Molecular
> >>>>> Universidad de Talca
> >>>>> Av. Lircay S/N, Talca, Chile
> >>>>> T: (+56) 712201 798
> >>>>> E: carlos.navarro87 at gmail.com o cnavarro at utalca.cl
> >>>>>
> >>>>> On March 17, 2016 at 11:07:48 AM, James Starlight (
> jmsstarlight at gmail.com) wrote:
> >>>>>
> >>>>> Dear Gromacs users!
> >>>>>
> >>>>> I wonder to ask for some suggestions about possibility of the CG to
> >>>>> full atomistic conversion of sample pdb files extracted from the CG
> >>>>> (Martini based) md trajectories. I will be especially thankful for
> any
> >>>>> kind of the useful tutorial focused on the subject.
> >>>>>
> >>>>> Thanks for help in advance!
> >>>>>
> >>>>> J.
> >>>>> --
> >>>>> 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-request at 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-request at 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-request at 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-request at 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-request at gromacs.org.