Hi Justine, As you can see in my .itp file the atom number starts from 1. Even this is the case with index file. I tried to modify index file to have atomic number same as pdb file but it gave a blank output. So my first concern is how GROMACS will know which atom I want to restrain? shall I change the atom number in itp file to corresponding atom number in pdb? My second concern is the second line of my .itp file looks different from the one given in GROMACS website As per GROMACS website:
; ai aj type index type’ low up1 up2 fac in my generated itp: ; i j ? label funct lo up1 up2 weight So what do you suggest me to do? Thanks in advance. -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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.
