[gmx-users] generating martini-version of lipids

[Tsjerk Wassenaar]

Hi Jagannath,

Can you send me (off-list) the mapping file and the atomistic structure?
Then I'll have a look.

Best,

Tsjerk

On Tue, Mar 1, 2016 at 11:08 AM, jagannath mondal <jm3745 at columbia.edu>
wrote:

> Hi Tsjerk
>
>    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
> Mapping folder.
>  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:
>
> /home/jmondal/CG_MARTINI_Backup/MARTINI_BETA_PEPTIDE_REVISITED/New_martini_tools/BACKWARD/Mapping/leu.charmm36.map).
> 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
> issue.
> 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 ]
> DPPG
>
> [ martini ]
> GL0 PO4 GL1 GL2 C1A C2A C3A C4A C1B C2B D3B C4B C5B
>
> [ mapping ]
> charmm36
>
> [ 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>
> wrote:
>
> > Hi Jagannath,
> >
> > Backward actually can do both. For conversion of a Gromos system use
> >
> > backward.py -from gromos -to martini
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> >
> > 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
> > the
> > > 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
> > version
> > > 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
> > the
> > > atomistic lipid bilayer/water, that will be very helpful.
> > >
> > > Jagannath
> > > --
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> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
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-- 
Tsjerk A. Wassenaar, Ph.D.