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

[James Starlight]

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.
>>>>> --
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