[gmx-users] adding NH2 cap to C terminal

sarbani chattopadhyay sarbani_c84 at rediffmail.com
Mon Nov 10 11:00:01 CET 2008

  Thank you for reply.
  Amber  force fields have parameters for C-terminal-C(O)-NH2 . But I don't know which of 
the force fields in Gromacs 3.3.1 have parametrs for the C-terminal amide cap. Is it 
possible to introduce these parameters manually. What I need to know is that which other 
files  do I need to modify ?
Till now I have only modified the terminal database ,( though I may have made some 
mistake ), but the added "N" 's coordinates are given by pdb2gmx  as " nan nan nan"

Thanks in advance

On Mon, 10 Nov 2008 Mark Abraham wrote :
>sarbani chattopadhyay wrote:
>>   Hi,
>>     I want to add -NH2 to the c terminal end of my peptide. If I modify the " C-terminal
>>databse"-> "-c.tdb" , will it be possible to add -NH2 to the "CO" end of the last residue 
at the
>>C terminal end.
>For some forcefields, yes. You need the forcefield to have parameters for (C-terminal) -C
(O)-NH2. Not all of them do. Probably the ones that have it parameterized already have the 
terminus topologies in the database.
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