Hello All I am trying to perform MD for protein-ligand complex in POPC with charmm36 force field and also follow Justin A. Lemkul tutorial using Gromacs VERSION 4.5.5.
As I am working on Protein-Ligand complex I am having few queries: 1) The .pdb file was oriented along the z-axis using editconf -princ, followed by a rotation. We have to perform this step before separating the protein and ligand from the pdb file so that ligand also rotated along the same axis?? 2) For orientation I use the following command. editconf -princ -f protein.pdb -o protein_princ.pdb editconf -rotate 0 0 90 -f protein_princ.pdb -o protein_princ_rotate.pdb But when I include the POPC then saw that The protein is parallel align with popc which is not correct. I also use editconf -rotate 0 90 0 -f protein_princ.pdb -o protein_princ_rotate.pdb but still the alignment is same. Should I use only editconf -princ command and skip the rotation part or what else I can do?? 3) As* InflateGRO* script can not deal with ligand. So when should I include my ligand file in protein?? I have included it before system creation and at the time of using *InflateGRO* script I remove my ligand file and again insert it after perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat before solvating the system with water. Is this the right way or I have to do it by another way?? Please Help. With Regards Neha Bharty -- 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.