[gmx-users] adding new lipid into /charmm27.ff/lipids.rtp

[Justin A. Lemkul]

Bing Bing wrote:
> Dear All,
> Hi! I 'm using Charmm-gui to generate an empty membrane pdb and toppar, 
> i managed to get the charmm topology from toppar directory. With that, 
> I'm trying to put additional lipid topology from charmm-gui  into 
> /charmm27.ff/lipids.rtp (gromacs4.5.4) for my empty membrane. But with 
> pdb2gmx, it failed to recognize the residue type with the error "Residue 
> not found in residue topology database".
> May i know in the rtp file format,  is the spacing crucial in order for 
> gromacs to process?
> 

Manual section 5.6.1.  You can use the other .rtp entries in the force field as 
a guide.  Whitespace is unimportant.

Note that you may get a mess of topologies if you run pdb2gmx on a complete 
membrane, especially if the it's a pure membrane.  pdb2gmx is intended for 
construction topologies from repeat units, e.g. to build proteins and other 
(mostly) linear polymers.  If you want to use pdb2gmx, you're better off doing 
so an a coordinate file of a single lipid and using that as an #included 
topology in the system .top.  Much cleaner.

-Justin

> thank you in advance.
> 
> 
> best regards,
> bing
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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