On 11/2/14 5:02 AM, Somayeh Alimohammadi wrote:
Dear gmx users I am performing a simulation protein- ligand by gromacs. this protein contain two chains (A & B) which separated from eachother. I did the following steps for pdb file 1- pdb2gmx –ignh –f initial.pdb –o initial.pdb –p topol.top -ter 2- editconf -bt cubic –f initial.pdb –o initial.pdb -c –d 0.9 3- genbox –cp initial.pdb –cs spc216.gro –o initial-box.pdb –p topol.top 4- grompp –f em.mdp –c initialbox.pdb –p topol.top –o xion.tpr 5- genion -s xion.tpr -o initial_ions.gro -p topol.top -pname NA -nname CL -nn (number of charge) everything was perfect, but the final pdb file has a problem which two chains are connected eachother. I would like to know how to solve these problems?
If the two chains have unique chain identifiers in the starting .pdb file, and you don't use pdb2gmx -merge to create any sort of inter-molecular disulfides or anything, the chains are not connected. If there are "bonds" showing up in VMD or something, those usually aren't real because VMD isn't always smart. If there is something else going on, please provide evidence of what you mean (topology output or whatever else).
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
