[gmx-users] I need 256 lipids ...
David van der Spoel
spoel at xray.bmc.uu.se
Fri Dec 1 15:22:28 CET 2006
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 ?
>> 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,
maybe you can forward your "corrected" files to Peter Tieleman, since
this is where people look for these files.
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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