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

Stéphane Téletchéa steletch at jouy.inra.fr
Thu Nov 30 17:57:12 CET 2006

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 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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