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

Thu Mar 17 17:32:10 CET 2016

Hi James,
Sadly I have no idea. I have never used that method/approximation before.
Hope someone with more experience can answer your last question.
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 1:26:24 PM, James Starlight (jmsstarlight at gmail.com) wrote:

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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