RE: AMBER: Adding residues

From: Ross Walker <>
Date: Mon, 9 Aug 2004 11:50:59 -0700

Dear Yen,
Your question is not totally clear but what I think you are asking is can
you replace the C or N terminal of a protein with a normal residue and then
add extra residues that end in a C or N terminal.
In principle yes you can, simply edit your pdb and add the N atoms of the
extra residues at the end of the chain in "reasonable" positions. Xleap will
then add the missing atoms for you. You can then select these residues in
xleap and relax their structure. If your original C or N terminus was on the
edge of a protein then you should be ok. If however it is buried you are
likely to have a large number of steric clashes. Either way you are going to
have to very carefully minimise your system, probably in several stages with
varying restraints on the new parts you added. You will then probably need
to run 20ps or so of MD at low temperature, 20K or so with the time step set
very small, probably 0.5fs or less. This will allow you system to re-arrange
and relax to accomodate the extra resiudes. You can then try slowly heating
your system and running equilibration at 300K. Don't surprised however if
your system "blows up" during this stage. You may have to try several
different initial structures to find one that you can simulate stably. You
may also want to set vlimit to something small like 5 during the 20ps at low
temperature stage, in this way any atoms that have steric clashes and gain
large velocities may be prevented from travelling too far.
Your best bet is to try it and see.
All the best
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |


From: [] On Behalf Of
yen li
Sent: 09 August 2004 10:48
Subject: AMBER: Adding residues

Hello all,
Is there any way in amber by which I can add some residues to either N or
C-terminal of a protein, so that the resultant protein is big with some more


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Received on Mon Aug 09 2004 - 19:53:01 PDT
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