[gmx-users] Re: Running Lyz in water

[Justin A. Lemkul]

Ravi Kumar Venkatraman wrote:
> 
> 
>    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.
> 

In the genbox step, the topology is both input and output, since it is modified 
by the program.  You still haven't posted the exact command you tried, but if 
you did what the tutorial said, it would have worked.  I know because several 
hundred people have gone through the tutorial successfully.

Either you named the file differently or perhaps placed it in a different 
directory such that genbox can't find it, but if you did indeed follow the 
tutorial exactly, this should not happen.

-Justin

> 
> 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*
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================