[gmx-users] CG to AA backmapping: problem in using initram.sh script

Sudip Das das.sudip37 at gmail.com
Mon Jul 17 11:41:26 CEST 2017

Dear All,

I forgot to mention one point in my previous mail.

With the system containing only one detergent molecules gives me the
following error, without generating any output file.

Residues defined for transformation from martini to gromos54a7:
Traceback (most recent call last):
  File "/home/CG2AA/backward1/backward.py", line 821, in <module>
    raise ValueError, "Unknown residue: %s\n"%resn
ValueError: Unknown residue: DET

Best regards,

On Mon, Jul 17, 2017 at 3:04 PM, Sudip Das <das.sudip37 at gmail.com> wrote:

> Dear All,
> I have carried out CGMD simulation of my system consist of a protein along
> with 30 detergent molecules. I have used Martini parameters along with the
> ELNEDYN model for protein.
> Now I am trying to get back AA coordinates from the CG structure using
> initram.sh script together with GROMACS 5.0.5 (double precision) with the
> below execution command:
> ./initram.sh -f CG.gro -o AA_gromos.gro -from martini -to gromos54a7 -p
> AA.top
> It can find out the dependencies:
> Checking dependencies:
> backward.py ... /home/CG2AA/backward.py
> gmx_mpi_d ... /home/sudip/softwares/gromacs-5.0.5/build/bin/gmx_mpi_d
> Even though this gives me the following errors:
> Error reading amber to martini mapping for GMO (file:
> /home/CG2AA/Mapping/sol.gromos.map).
> .
> .
> .
> Fatal error:
> number of coordinates in coordinate file (0-backward.gro, 107331)
>              does not match topology (backmapped.top, 108471)
> Now, 108471 - 107331 = 1140, which is same as the number of atoms in 30
> detergent molecules.
> In the 0-backward.gro file, coordinates for protein, water and ions are
> written, but coordinates for detergent are absent even though the
> initram.sh script can find out the detergent mapping scheme (DET) within
> the /Mapping directory.
> Residues defined for transformation from martini to gromos54a7:
> ['POPC', 'GLN', 'ILE', 'POPE', *'DET*', 'POPS', 'GLY', 'GLU', 'CYS',
> 'HIS', 'SER', 'SEP', 'PRO', 'CHOL', 'CL4', 'ASN', 'HEP', 'VAL', 'DOPE',
> 'DPPC', 'DOPC', 'THR', 'ASP', 'TRP', 'LYS', 'PHE', 'ALA', 'MET', 'LEU',
> 'ARG', 'TYR']
> I want to transform coordinates from Martini to gromos. Then why does the
> error message "Error reading amber to martini mapping for GMO" tell about
> amber?
> I have also tried the same protocol with only one detergent molecule as my
> system. But, still I got the same error.
> Please help me to resolve this.
> Thanks in advance for your kind help.
> N.B.: I have registered in the cgmartini site, but I am unable to find out
> how to post a query there. So I have posted here. Sorry!
> Best regards,
> Sudip

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