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
--
Stéphane Téletchéa, PhD. http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901
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