[gmx-users] adding NH2 cap to C terminal

[Justin A. Lemkul]

sarbani chattopadhyay wrote:
>   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"
> 

I think you are going about this the wrong way.  The first question is - do you 
have the amide intact in the .pdb file?  If not, pdb2gmx is not going to add it 
in for you magically.  You can find out which force fields contain parameterized 
NH2 groups if you just search the .rtp files with a text editor.  Offhand, I 
know that the Gromos force fields support C-terminal amides, but probably others 
do as well.

-Justin

> Thanks in advance
> Sarbani
> 
> 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.
>  >
>  >Mark
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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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