[gmx-users] Minimization problem, again!

[andrea spitaleri]

Hi,
of course. In fact, when you use genbox, few lipid are removed. You have 
to take in account of this and edit your topology file.

Regards,

andrea

liu xin wrote:

> Hello Viswanadham and Andrea,
>
> My protein is generated from our lab, I use dppc128 membrane.
>
> After I use genbox to remove clashes, I use genbox again to solvate my 
> lipid/protein system in water, but when I do grompp there comes 
> another error:
> ##########################################################################
> Fatal error: number of coordinates in coordinate file (merge.gro, 
> 115120) does not match topology (merge.top, 116570)
> ########################################################################## 
>
> I download the dppc128 top file from the websit, and generate the 
> protein top file by hand, then I make them as a whole top file for my 
> lipid/protein system, cause there's a error when I use pdb2gmx to 
> generate a top file for the whole system.
> If I  choose to use the download top file for my bilayer, how can I 
> solve this problem?
>
> Thanks in advance!
>
> On 12/15/05, *Viswanadham Sridhara* < muta.mestri at gmail.com 
> <mailto:muta.mestri at gmail.com>> wrote:
>
>     Hi Andrea and Liu,
>     Since you are discussing this topic, I have a general Question.
>     1.) What is the protein you are using( any ID of the protein to
>     search in protein data bank), and
>     2) what kind of membrane is it?(DPPC, DOPC??)
>     And how big is your initial membrane(128 , 256 or 512 lipids??).
>     Thanks in advance,
>     Viswam.
>
>     On 12/15/05, *andrea spitaleri* < spitaleri.andrea at hsr.it
>     <mailto:spitaleri.andrea at hsr.it>> wrote:
>
>         Hi Liu,
>         I explain it a bit better.  Basicaly I create my system
>         protein/membrane with vmd, not taking in account possible
>         clashes. Afterwards, I use the gromacs tools, genbox, in order
>         to solvate the protein with the membrane as well described here:
>         http://www.dddc.ac.cn/embo04/practicals/9_16.htm
>         genbox remove in such way eventual clashes.
>
>         I hope this is a bit clearer
>
>         Regards
>
>         andrea
>
>
>         -- 
>         -------------------------------
>         Andrea Spitaleri
>         Dulbecco Telethon Institute
>         c/o DIBIT Scientific Institute
>         Biomolecular NMR, 1B4
>         Via Olgettina 58
>         20132 Milano (Italy)
>         Get Firefox!
>         <http://www.spreadfirefox.com/?q=affiliates&id=0&t=85>
>         -------------------------------
>
>         _______________________________________________
>         gmx-users mailing list
>         gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>         http://www.gromacs.org/mailman/listinfo/gmx-users
>         Please don't post (un)subscribe requests to the list. Use the
>         www interface or send it to gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>.
>
>
>
>
>     -- 
>     Viswanadham Sridhara,
>     Graduate Research Assistant,
>     Old Dominion University, "VIRGINIA".
>
>     _______________________________________________
>     gmx-users mailing list
>     gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>
>
>------------------------------------------------------------------------
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>

-- 
-------------------------------
Andrea Spitaleri
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Get Firefox! <http://www.spreadfirefox.com/?q=affiliates&id=0&t=85>
-------------------------------