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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Nov 7 00:36:33 CET 2008

Justin A. Lemkul wrote:
> 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.

... and the forcefield must be parameterized to have such a group in it. 
Check the contents of the .rtp file.


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