[gmx-users] Re: Running Lyz in water

[Ravi Kumar Venkatraman]

   Dear all,
                I am not finding mistake in that tutorial but I wanted to
know where did I go wrong. Until generation of topology for protein there
was no problem (I cross checked with the tutorial).
After that I edited the box of protein as such. After generating the
solvation box I having problem. At least let me know is there different
command for input /output *.top file in genbox. Please help me in this
regard.


Thank you.




Dear all,
>             I have been running lyz in water. I have 20 ps pre-equilibrated
> NVT and 200 ps NPT configuration of spce216 water. I am following the
> instruction from gromacs tutorial. This is the link for the tutorial,
>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
>
> After editing the box for lyz and then I tried to solvate the box with
> spce216 water. I followed the same instruction but it shows fatal I/O error
> - topol.top. It was not able to find the input file topol.top. But in this
> tutorial its an output command. Further it shows 6091 solvent instead of
> 10832 as per tutorial. Pls help me find the problem.
>
> Thank you
>
> *With Regards,**
> *
> *
> *
> *Ravi Kumar Venkatraman,*
> *c/o Prof. Siva Umapathy,**
> *
> *IPC Dept., IISc.,*
> *Bangalore, INDIA.*
> *Phone No: +91-9686933963*
>
>


-- 
*With Regards,**
*
*
*
*Ravi Kumar Venkatraman,*
*c/o Prof. Siva Umapathy,**
*
*IPC Dept., IISc.,*
*Bangalore, INDIA.*
*Phone No: +91-9686933963*
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