[gmx-users] Problem in making index.ndx and disres.itp

[Tushar Ranjan Moharana]

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