[gmx-users] files to modify to add NH2 cap at C terminal end

Mark Abraham Mark.Abraham at anu.edu.au
Mon Nov 10 13:24:55 CET 2008

sarbani chattopadhyay wrote:
>   Hi everyone,
>                     I had asked this question before but I will try to 
> explain myself more clearly.
> I wan t to add -NH2 cap at the Cterminal end of my protein. I had 
> included "charmm" force
> field into my gromacs 3.3.1.
> I had added the following into my ffcharmm-c.tdb file
> [NH2]
> [replace]
> O            OB        15.994  -0.550
> CA            CT1        12.0110  0.070
> C            CD        12.0110  0.720
> [add]
> 1    4        NH2  C  CA  C
>       NH2      14.0027 -0.7800
> 2    3        HT    N CA  C
>       HT      1.0080 0.3100
> However, the coordinates of the added N is given by "pdb2gmx" as " nan 
> nan nan".

nan = Not a Number, i.e. pdb2gmx was unable to compute the position of 
your N atom. The three control atoms i,j,k have to be different, since 
you need three unique pieces of information to isolate a point in 3D 
space. I'd be surprised if pdb2gmx didn't issue a warning about this, 
but perhaps the developers assumed that someone willing to edit the .tdb 
would get it right!


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