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

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 10 13:24:39 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

I don't know what add type 4 is in the context of a C-terminal database, but in 
the .hdb it means to add two or three tetrahedral H atoms.

> 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".

Are they present in the input structure?  If you're trying to add them through 
this mechanism, it probably won't work.

> If anyone can give any suggestion to fix this poblem, I will be highly 
> obliged.

The CHARMM .rtp that I have (from the User Contributions site) contains a 
parameterized NH2 residue.  That means, if the amide is present in the .pdb file 
you have, then all you have to do is give pdb2gmx -ter and select 'None', 
instead of messing around with the .tdb files.


> Thanks in advance,
> Sarbani
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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