sunny mishra wrote:
Hi all,
After inserting the protein into the lipid bilayer I am working on
inflategro script and trying to scale the lipid and do energy
minimization. Since I am doing everything in CG so I dnt know whether
inflategro is defined for CG or not? Besides that when I run the script
provided
in http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis , I
don't know why I am getting these errors and what is the issue behind that.
My errors are something like this:
Use of uninitialized value $box_x in multiplication (*) at ./INFLATEGRO
line 259
Use of uninitialized value $box_y in multiplication (*) at ./INFLATEGRO
line 260
Scaling lipids....
There are 0 lipids...
Illegal divison by zero at ./INFLATEGRO line 300
I have no idea about this. Please help me out.
InflateGRO is hard-coded to search for "P" atoms, common to phospholipids. You
might have to change the pattern matching specification to detect some (unique)
atom in your lipid.
It also looks like there is a problem with the box definition. Do you have
appropriate box vectors defined in your input .gro file?
-Justin
Thanks,
Sunny
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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