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

[Mark Abraham]

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.

Mark