GROMACS version: 2020.4
GROMACS modification: Yes/No
I’ve tried to build a protein with residue 407 embeded POPC bilayer.
As my protein is lager than POPC128.pdb (from http://wcm.ucalgary.ca/tieleman/downloads), I needed to generate larger POPC membrane.
I added single POPC molecule in popc128.pdb for each leaflet, concatenated protein.gro file and popc.gro file, and used ‘inflategro.pl’ file. But the some unexpected messages are raised as below:
…
Use of uninitialized value in addition (+) at /home/byun/PROject/APP-complex/GROMOS-ff/GADGET/inflategro.pl line 496.
Use of uninitialized value within @overlap in numeric eq (==) at /home/byun/PROject/APP-complex/GROMOS-ff/GADGET/inflategro.pl line 500.
Argument “A2” isn’t numeric in printf at /home/byun/PROject/APP-complex/GROMOS-ff/GADGET/inflategro.pl line 502.
…
And inflategro.pl identified the wrong number of popc molecules…
My system has 8126 popc molecules but the verbose message showed There are 3782 lipids...
The figure below is output(system_inflated.gro)
How can I solve this problem?
Thank you for considering my question :)