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On 19/02/2012 7:26 PM, Banafsheh Mehrazma wrote:
<blockquote
cite="mid:CADNrWT7cHcbX9HsSw8ZOA5W+Bii3B=Z9Bft-h=xsEaT5Fpw+4g@mail.gmail.com"
type="cite">Dear Mark
<div><br>
</div>
<div>Thanks for your reply</div>
<div><br>
</div>
<div>You said "These should function the same", are results of
parm 99 and amber 99 the same?</div>
<div>Please explain more about (but you should check yourself that
each cites the same literature).</div>
</blockquote>
<br>
Random files that you find with software implement some model that
was hopefully published somewhere. If those files (or the associated
documentation) each claim the same published source, then you have
grounds for knowing they're the same. Some random person on the
internet telling you they're the same is next to useless :-)<br>
<br>
<blockquote
cite="mid:CADNrWT7cHcbX9HsSw8ZOA5W+Bii3B=Z9Bft-h=xsEaT5Fpw+4g@mail.gmail.com"
type="cite">
<div><br>
</div>
<div>One more thing, I want to transfer Force Constant Kθ (kcal/
mol rad2) and Equilibrium Bond Angle θeq (º) from PARM99 TO
AMBER99, however there are no such factors in ffbonded.itp in
ffamber99, I looked through chapter 4, but didn't get any clue
of what I should do. <br>
</div>
</blockquote>
<br>
Chapter 4 explains the function types and chapter 5 explains the
file formats. You'll need to understand the relevant parts of both,
and get the unit conversion right (chapter 2). And do a bunch of
GROMACS tutorial material before even thinking about modifying force
fields. :-)<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CADNrWT7cHcbX9HsSw8ZOA5W+Bii3B=Z9Bft-h=xsEaT5Fpw+4g@mail.gmail.com"
type="cite">
<div><br>
</div>
<div>Best regards.</div>
<div>Banafsheh</div>
<div><br>
<div class="gmail_quote">On Sat, Feb 18, 2012 at 5:11 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb">
<div class="h5">On 18/02/2012 7:23 PM, Banafsheh Mehrazma
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear all;<br>
I am wondering if the amber99 in gromacs package is
the same as PARM99<br>
in Amber package, so that I can use the new modified
parameters (which<br>
is made in Amber package) in my simulation in gromacs?
Or should I<br>
make some changes?<br>
</blockquote>
<br>
</div>
</div>
These should function the same - but you should check
yourself that each cites the same literature.<span
class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
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