[gmx-users] About Area per lipid using Gid-MAT

Justin Lemkul jalemkul at vt.edu
Thu Nov 17 17:10:48 CET 2016

On 11/17/16 11:09 AM, Poncho Arvayo Zatarain wrote:
> Hello: I'm calculating the area per lipid of a mixed bilayer of dppc and dppe with a molecule inside, using GRID MAT. When i run Grid Mat it appears: Can't calculate the are per lipid, line 761 can't divided by zero in GRID-MAT-MD.pl. So, i check de Grid-MAT.pl in line 761 and this is in: Which is the line that indicates can't divided by zero or which i have to modificate?
> # Print APLs just based on number of lipids and cross-sectional surface area
>     print "\nCalculating area per lipid head group...\n";
>     my $area = $transfer_x*$transfer_y*100;
>     my $area_per_lipid_top = $area/(scalar(@top_leaflet_ref));
>     my $area_per_lipid_bottom = $area/(scalar(@bottom_leaflet_ref));
>     printf ("The lateral area of the system is %.5f sq. Angstroms (per side)\n", $area);
>     print "When you don't account for any protein atoms:\n";
>     printf ("    The average area per lipid in the top leaflet is %.5f sq. Angstroms\n", $area_per_lipid_top);
>     printf ("    The average area per lipid in the bottom leaflet is %.5f sq. Angstroms\n", $area_per_lipid_bottom);
>     if ($param{protein} eq("yes")){
>         print "When you do take the protein atoms into account:\n";

Likely you're specifying your lipid residue name(s) incorrectly, but if you need 
to troubleshoot further, send me your coordinate and input files off-list and we 
can look at it further because this is not a GROMACS problem.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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