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

sarbani chattopadhyay sarbani_c84 at rediffmail.com
Mon Nov 10 12:00:38 CET 2008

  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
O             OB         15.994   -0.550
CA            CT1        12.0110   0.070
C             CD         12.0110   0.720
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".
If anyone can give any suggestion to fix this poblem, I will be highly obliged.

Thanks in advance,
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