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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
