[gmx-users] Inflategro for Coarse Grained

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 28 22:15:53 CET 2009

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?


> Thanks,
> Sunny
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list