[gmx-users] Weird structure after minimization (membrane proteinsimulation

[Mark Abraham]

alokjain at iitk.ac.in wrote:
> Dear Mark, & Chris,
> 
> Thanks for your useful suggestions.
> 
> Yes Mark define = -DFLEXIBLE is the only difference in both the cases.
> 
> Actually in my previous post I have pasted only small section of tip4p.itp
> file,(sorry if it created unnecessary confusions/doubt). This time I am
> pasting full tip4p.itp file. As you expected, it has more #ifdef statements.

OK

> I have not modified this file. this is the original file and comes with the
> gromacs-3.2.1 distribution. I have cross checked it with the clean
> distribution.

Is this distribution the only one you have installed? If not, you want 
to take care that GMXLIB is pointing to the right spot so that you're 
actually including the .itp files you think you are.

I realise that make_hole requires some early version of GROMACS, but 
once it has been run, perhaps you should take its output structure and 
use a 3.3.x version from there.

> I have also compared the order of TIP4P atoms in my structure file
> (gro/pdb) and the same is pasted below as TIP4P.itp file. Order is same in
> both the
> files.

OK, well there goes that idea.

Mark