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

[Sudip Das]

Hi Peter,

The path of my mapping file is: /home/CG2AA/Mapping/det.gromos.map

The structural sequence of my detergent is: HO-(CH2-CH2-O)8-(CH2)11-CH3
 (Basically a C12EO8, i.e., polyethylene-glycol (PEG) with C12 hydrophobic
tail).

The content of det.gromos.map file is as below:

[ molecule ]
DET

[ martini ]
OH  O11  O12  O13  O14  O15  O16  O17  O18  C1 C2 C3

[ mapping ]
gromos54a7

[ atoms ]
    1   H     OH
    2   OA    OH
    3   CH2   O11
    4   CH2   O11
    5   OE    O11
    6   CH2   O12
    7   CH2   O12
    8   OE    O12
    9   CH2   O13
   10   CH2   O13
   11   OE    O13
   12   CH2   O14
   13   CH2   O14
   14   OE    O14
   15   CH2   O15
   16   CH2   O15
   17   OE    O15
   18   CH2   O16
   19   CH2   O16
   20   OE    O16
   21   CH2   O17
   22   CH2   O17
   23   OE    O17
   24   CH2   O18
   25   CH2   O18
   26   OE    O18
   27   CH2   C1
   28   CH2   C1
   29   CH2   C1
   30   CH2   C1
   31   CH2   C2
   32   CH2   C2
   33   CH2   C2
   34   CH2   C2
   35   CH2   C3
   36   CH2   C3
   37   CH2   C3
   38   CH3   C3


Thanks for your kind and prompt reply!

Best regards,
Sudip




On Mon, Jul 17, 2017 at 3:15 PM, Peter Kroon <p.c.kroon at rug.nl> wrote:

> Hi Sudip,
>
>
> what's the path and content of your DET mapping file?
>
>
> Peter
>
>
> On 17-07-17 11:41, Sudip Das wrote:
> > 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,
> > Sudip
> >
> >
> >
> > 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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