[gmx-users] CCL4 Solvent box

[David]

On Mon, 2003-03-31 at 18:09, Venkat Ramanan K wrote:
> Hi,
> 
> I am an Undergraduate student at Centre for Biotechnology, anna  
> University. Presently I am doing my project, and it involves 
> Molcular  dynamics simulation of Candida rugosa Lipase in CCL4 
> enviornment. I  have set up a cluster of 16 nodes using LAM and 
> using GROMACS 3.1 for  the simulation.
> 
> I have just started off with the dynamics part, in which I have to  
> generate a solvent box filled with CCL4. I tried to get the pdb 
> file  of the ccl4 molecule and tried to generate the required .gro 
> file. It  works but when i do the grompp step I get teh following 
> error.
> 
> Fatal error: number of coordinates in coordinate file (b4em.gro,
>              5391)
>              does not match topology (1crl.top, 5126)
> 
> Please help me out with this. If you have a .gro file of the CCl4  
> solvent which replaces the default spc216.gro, please send it to 
> me.  And also instruct me on the steps I should follow to run this  
> simulation in CCl4 box.
If you don't have a box of CCl4 yet, (and can't find one) make a single
molecule, minimize it, and then use genconf to generate a larger box,
the do MD with pressure coupling to get the density right. The resulting
box can then be used for genbox, to solvate your protein.

> 
> Venky
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel
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