[gmx-users] DPPC,Water,Protein-?

[Stud_Psychopharm]

Dear All,
I could able to get 128 DPPC (lipid) with water molecules from tielemans 
site, now I want place my protein (tetramer) into that by removing some 
number of lipid and water molecules. Is there any program to do that job. 
Please give soem idea. Many thanks in advance.
Regards,
Blaise M Costa.
------------------------------------------------------------
"The more we learn the more we realize how little we know." - 
R.Buckminster Fuller 

Blaise M.
Graduate Student,
Department of Psychopharmacology,
National Institute of Mental Health And Neuro Sciences (NIMHANS),
Bangalore-560029,
India. Tel: 91 80 6995112.


-----Original Message-----
From: Anton Feenstra <feenstra at chem.vu.nl>
To: gmx-users at gromacs.org
Date: Mon, 27 Oct 2003 18:28:02 +0100
Subject: Re: [gmx-users] xtc vs trr format

> Nuno R. L. Ferreira wrote:
> 
> > Hello gmx users
> > 
> > By default mdrun saves .xtc files, so I assume that a great majority
> of you
> > save the trajectories in this format.
> > Is that right? And what about -ndec, do you use 3 or a greater
> precision?
> > I think that we have to choose the precision accordingly to what we
> want to
> > digg out from the trajectory.
> > 
> > I'm performing some normal MD stuff, and it's time to save my
> information.
> > My trajectories are in .trr format,  and just wanted to ask for an
> opinion
> > about a "safe" format to put in the CD (several, by the way).
> > After that, the analyses could be made in any other precision.
> 
> I use the default ndec=3, that is sufficient for all types of analysis
> that I ever heard of. I tune nstxout/nstvout so that a frame is written
> to .trr file every few hours along the calculation (usualy every
> 10-50ps).
> Depending on how much disk is on the machine I run on, I either write
> the
> whole system to .xtc every 1 ps, or I only write protein(s) +
> substrate(s) +
> co-factor(s). That, I also put on CD (or, recently, on DVD!). Then, I
> make
> one .xtc file with only the 'protein+stuff' in it (if I haven't got
> that
> already), and a few ones with less frames, like every 10 ps and every
> 100ps,
> which I can use for quick analysis (e.g. an rmsd plot).
> 
> 
> -- 
> Groetjes,
> 
> Anton
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
> |             | "If You See Me Getting High, Knock Me Down"           |
> |             | (Red Hot Chili Peppers)                               |
> |_____________|_______________________________________________________|
> 
> 
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