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

Sudip Das das.sudip37 at gmail.com
Mon Jul 17 11:34:25 CEST 2017

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

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:
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',

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

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,

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