[gmx-users] I need 256 lipids ...

[David van der Spoel]

Stéphane Téletchéa wrote:
> David van der Spoel a écrit :
>>> Stéphane Téletchéa wrote:
> 
>>> editconf -f dppc64.pdb -o dppc64_pbc.pdb -pbc
>>>
>>> But unfortunately, some lipids are not imaged (at least 18, 25 and 
>>> 53). I tried using trjconv but it needs a topol.tpr that i don't have 
>>> :-(
>>>
>>> Any hint ?
>>>
>>> Stéphane
>>>
>> It requires some manual work, but with editconf you can translate a 
>> subset of atoms, so you have to find out which atoms they are, and 
>> then write an index file, and then translate them by one box.
> 
> It works now !
> 
> Just for the record, here are the steps i did to obtain a usable file:
> 
> 1 - editconf -f dppc64.pdb -o dppc64_pbc.pdb -pbc
> 
> At this step, 4 lipids are not correctly imaged (18, 23, 25 and 53). The 
> problem is the same for all of them, one palmitoyl tail is not imaged to 
> its counterpart. I presume this comes form the way the algorithm tries 
> to guess the tail to image.
> 3 DPPC (18,25 and 53) need to get their tail back via a -x translation, 
> DPPC 23 needs a -y translation. To perform this:
> 
> 2 - editconf -f dppc64_pbc1.pdb -o dppc64_pbcx.pdb -n grouptomove_x.ndx 
>  -translate -4.7245 0 0
> 
> 3 - editconf -f dppc64_pbc1.pdb -o dppc64_pbcy.pdb -n grouptomove_y.ndx 
> -translate 0 -4.2319 0
> 
> 4 - edit manually the files to correct the coordinates.
> 
> If there's a need, i can do a better explanation and provide files on my 
> website, feel free to ask.
> 
> Thanks for the help,
> 
> Stéphane
> 
maybe you can forward your "corrected" files to Peter Tieleman, since 
this is where people look for these files.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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