[gmx-users] adding NH2 cap to C terminal
Justin A. Lemkul
jalemkul at vt.edu
Mon Nov 10 13:17:09 CET 2008
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.
> 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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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