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