[gmx-users] CG to AA backmapping: problem in using initram.sh script
das.sudip37 at gmail.com
Mon Jul 17 13:01:54 CEST 2017
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
The content of det.gromos.map file is as below:
[ molecule ]
[ martini ]
OH O11 O12 O13 O14 O15 O16 O17 O18 C1 C2 C3
[ mapping ]
[ 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!
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?
> 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>
> >> Dear All,
> >> I have carried out CGMD simulation of my system consist of a protein
> >> with 30 detergent molecules. I have used Martini parameters along with
> >> 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
> >> 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
> >> error message "Error reading amber to martini mapping for GMO" tell
> >> amber?
> >> I have also tried the same protocol with only one detergent molecule as
> >> 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
> >> how to post a query there. So I have posted here. Sorry!
> >> Best regards,
> >> Sudip
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