Hello All I am trying to perform MD for protein-ligand complex in popc lipid with Charmm36 force field and also follow Justin A. Lemkul tutorial. I performed
perl inflategro.pl system.gro 4 POPC 0 system_inflated.pdb 5 area.dat followed by energy minimization then, perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat followed by energy minimization then after 16 iteration of scaling down by 0.95 I got Area per lipid: 1.00 nm^2. In 17th iteration Area per lipid become 0.80 nm^2. but after that when I visualize the .gro file i.e system_shrink17.gro the ligand molecule is far from protein and out of lipid. But till 16th iteration its inside the lipid in its normal position. Should I perform till 16th iteration which gives area per lipid 1.00 nm^2 ? Is it a good value for Area per lipid ?? or there is some error in my files. My topology file is : ; Include forcefield parameters #include "charmm36_lipid.ff/forcefield.itp" ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include ligand topology #include "LIG.itp" ; Ligand position restraints #ifdef POSRES #include "posre_LIG.itp" #endif [ moleculetype ] ; Name nrexcl Protein 3 [ atoms ] . . . . . . ; Strong position restraints for InflateGRO #ifdef POSRES_STRONG #include "strong_posre.itp" #endif ; Include POPC chain topology #include "popc.itp" ; Include water topology #include "charmm36_lipid.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "charmm36_lipid.ff/ions.itp" [ system ] ; Name Gyas ROwers Mature At Cryogenic Speed [ molecules ] ; Compound #mols Protein 1 LIG 1 POPC 128 Please Help Thank you very much. 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.