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!
Mark
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