[gmx-users] way to cap C-terminal as CONH2

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 6 16:28:50 CET 2008

sarbani chattopadhyay wrote:
>   Hi everyone,
>                     I want to know is there any way to add Amide cap at 
> the C terminal end of the
> protein using gromacs. Using "pdb2gmx -ter" doesnot give CONH2 as one of 
> the options.

The -NH2 group must be present in the .pdb file, and you choose "None" when 
prompted for the terminus.


> Any suggestion is welcome.
> 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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