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

[James Starlight]

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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