Dear Gromacs users I am doing a free energy calculation of the protein-ligand complex. During decoupling of the ligand vdw forces from protein, I have selected 21 different lambda windows between 0-1. I have put distance angle and dihedral restraints to keep the ligand in its position but in some of my lamda windows, the residue restrained with ligand crashes and generates different PDB structures. It crashes in lambda windows 0,1,2,4,8,9,11,12,13,17,18 however in windows 3,5,6,10, 14,15,19,20 it works well. My restraint section in topology is as below:-
; distance restraints [ bonds ] ; i j type r0A r1A r2A fcA r0B r1B r2B fcB 3437 7908 10 0.474 0.474 10.0 0.0 0.474 0.474 10.0 4184.000 [ angle_restraints ] ; ai aj ak al type thA fcA multA thB fcB multB 3437 7908 7905 7908 1 110.00 0.0 1 110.00 41.840 1 7908 3437 3439 3437 1 152.5 0.0 1 152.5 41.840 1 [ dihedral_restraints ] ; ai aj ak al type phiA dphiA fcA phiB dphiB fcB 7905 7908 3437 3439 1 140.19 0.0 0.0 140.19 0.0 41.840 7909 7908 3437 3439 1 -167.75 0.0 0.0 -69.05 0.0 41.840 7909 7908 3437 3433 1 -172.77 0.0 0.0 -172.77 0.0 41.840 Can anyone please suggest me how should I fix this? or where I am doing wrong? I will be really grateful. Thanks Sadaf Rani P.hD. visiting scholar Lancaster University Uk -- 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.
