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

[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.
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