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

[Peter Kroon]

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
>>