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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--
========================================
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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