[gmx-users] generating martini-version of lipids
jm3745 at columbia.edu
Tue Mar 1 11:08:23 CET 2016
I have created a "dppg.charmm36.map" file using the template provided by
popg and dppc mapping . Then I had put 'dppg.charmm36,map' file in the
However, If I want to do forward transformation i.e. going from charmm36
to martini , issuing the following command, it crashes:
./backward.py -f 1lip.gro -o 1lip_martini.gro -from charmm36 -to martini
"Error reading charmm36 to martini mapping for DPPG (file:
Residues defined for transformation from charmm36 to martini:
['POPC', 'ILE', 'POPG', 'GLN', 'POPS', 'GLY', 'GLU', 'CYS', 'ASP', 'POPE',
'LYS', 'PRO', 'CHOL', 'ASN', 'VAL', 'DPPC', 'DOPC', 'THR', 'HIS', 'TRP',
'SER', 'PHE', 'ALA', 'MET', 'LEU', 'ARG', 'TYR']
Traceback (most recent call last):
File "./backward.py", line 821, in <module>
raise ValueError, "Unknown residue: %s\n"%resn
ValueError: Unknown residue: DPPG "
However, I try the backword mapping option, it at least tries something
i.e. at least can locate dppg lipids. But, it 'bails out' due to some other
I think, for forward mapping I am missing out something.
Below I paste first few lines of my dppg.charmm36.map file that I created.
If you want, I can send you the files by email. But, I think all the
mapping files that are present in Mapping folder are meant for backward
mapping. Can you please check?
[ molecule ]
[ martini ]
GL0 PO4 GL1 GL2 C1A C2A C3A C4A C1B C2B D3B C4B C5B
[ mapping ]
[ atoms ]
1 C13 GL0
2 H13A GL0
3 H13B GL0
4 OC3 GL0
5 HO3 GL0
6 C12 GL0 GL0 GL0 PO4
7 H12A GL0
8 OC2 GL0
On Mon, Feb 29, 2016 at 10:10 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> Hi Jagannath,
> Backward actually can do both. For conversion of a Gromos system use
> backward.py -from gromos -to martini
> Hope it helps,
> On Mon, Feb 29, 2016 at 11:20 AM, Jagannath Mondal <
> jmondal.backup at gmail.com
> > wrote:
> > Dear Gromacs/Martini-users
> > I wanted to transform a snapshot of my atomistic DPPG/water bilayer to
> > Martini coarse-grained format. However, I found martinize.py script does
> > not transform lipid or waters to coarse-grained counterpart.It only works
> > for protein. So, Is there any particular way I can generate the CG
> > of my atomistic DPPG/water bilayer ?
> > I guess backward scripts does the reverse of what I am trying to achieve.
> > So, if you can suggest a way to generate a coarse-grained pdb files of
> > atomistic lipid bilayer/water, that will be very helpful.
> > Jagannath
> > --
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> Tsjerk A. Wassenaar, Ph.D.
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