Hello All I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial.
I generated small molecule topology file from SwissParam which provides .pdb file for ligand molecule. I don't have .gro file for small molecule thats why I have created all the file in .pdb file format. when I run: perl inflategro.pl system.pdb 4 POPC 0 system_inflated.gro 5 area.dat it gives error : Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids.... There are 0 lipids... How to work with .pdb file to run inflategro.pl command?? can anyone please help me out how to solve this error. Thanks in advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
