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On 20/07/2011 7:33 PM, sa wrote:
<blockquote
cite="mid:CAM9PwEP4kWHR_8SxdB2DuC9oVYcspy45tAyVC3FPNyTEjuZN+Q@mail.gmail.com"
type="cite">Thank you Austin, for the clarification,<br>
<br>
So my questions are: how to convert it in the gromacs format ? Is
it correct to use the absolute value of the multiplicity in my
parameters and use the negative values of barrier heights when
they are exist in the AMBER parameters? Since, I have noticed that
in the AMBER ff port in GROMACS, the multiplicity values are
always set to > 0 and the barrier heights have sometime a
negative value.<br>
</blockquote>
<br>
You want to implement the same mathematical function in each case.
Take the GLYCAM parameters, drop them into the correct function.
Then consult chapters 4 and 5 of the GROMACS manual and see what
will be necessary to reproduce that function. Then test on a tiny
system that you can also compute by hand to confirm your
understanding.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAM9PwEP4kWHR_8SxdB2DuC9oVYcspy45tAyVC3FPNyTEjuZN+Q@mail.gmail.com"
type="cite">
<br>
Thank you again for your advice.<br>
<br>
SA-<br>
<br>
<br>
<br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">
Message: 1<br>
Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT)<br>
From: "Austin B. Yongye" <<a moz-do-not-send="true"
href="mailto:ybausty@yahoo.com">ybausty@yahoo.com</a>><br>
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral
parameters<br>
in the GROMACS format.<br>
To: Discussion list for GROMACS users <<a
moz-do-not-send="true" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a moz-do-not-send="true"
href="mailto:1311098935.93905.YahooMailClassic@web161426.mail.bf1.yahoo.com">1311098935.93905.YahooMailClassic@web161426.mail.bf1.yahoo.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
It is normal to have combinations of negative and positive
values for the barrier heights. Those are just the best
coefficients to reproduce some QM rotational energy curve
during the parameterization. The negative periodicities are a
convention from AMBER. They simply indicate that the dihedral
angle potential has more than one term. For your example
below:<br>
<br>
O2-P<br>
-OS-CP 1 0.10 0.0
-3. Dimethyl phosphate<br>
1 -0.50 0.0
-2.<br>
<br>
1 0.10 <br>
0.0 1<br>
-3, -2 and 1 signify V3, V2 and V1 terms, respectively. Once a
positive value is reached, terms for the O2-P-OS-CP potential
have been completely accounted for.<br>
<br>
Hope that helps.<br>
Austin-<br>
<br>
<br>
--- On Tue, 7/19/11, Mark Abraham <<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>
wrote:<br>
<br>
From: Mark Abraham <<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral
parameters in the GROMACS format.<br>
To: "Discussion list for GROMACS users" <<a
moz-do-not-send="true" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Date: Tuesday, July 19, 2011, 7:08 AM<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
On 19/07/2011 11:56 PM, sa wrote:<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
Dear<br>
GROMCS users,<br>
<br>
I<br>
am trying to convert some GLYCAM parameters in
GROMACS format.<br>
For this<br>
purpose, I am using the latest GLYCAM parameters
downloaded<br>
from the RJ. Woods’<br>
website and the examples given in the acpype code
(here for<br>
the dihedral angles) :<br>
<br>
<br>
<br>
<br>
<br>
<a moz-do-not-send="true"
href="http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9&r=9&redir=1"
target="_blank">http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9&r=9&redir=1</a><br>
<br>
<br>
<br>
<br>
<br>
-------------------<br>
# dihedral idivf barrier hight/2 kcal/mol phase
degrees periodicity comments<br>
X -ca-ca-X 4 14.500*
180.000 2.000 intrpol.bsd.on C6H6<br>
<br>
* to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx,
no in topolbuild, why?) = 30.334 or 15.167 kJ/mol<br>
# X -CA-CA-X 4 14.50 180.0 2.
intrpol.bsd.on C6H6 (from parm99.dat)<br>
<br>
# X-CA-CA-X 3 30.33400 0.00000 -30.33400
0.00000 0.00000 0.00000 ; intrpol.bsd.on C6H6<br>
<br>
-----------<br>
<br>
I have no problems with the parameters for proteins. But,
in case of the GLYCAM parameters, I am a little confused<br>
<br>
about the conversion of dihedral force constants (DFC),
especially when the DFC and the periodicity values are < 0
for example<br>
for this torsion:<br>
<br>
<br>
O2-P<br>
-OS-CP 1 0.10 0.0
-3. Dimethyl phosphate<br>
1 -0.50 0.0 -2.<br>
<br>
1 0.10 <br>
0.0 1<br>
<br>
<br>
<br>
Where only a positive value makes sense, sometimes people
use<br>
negative values to indicate some special functional form.
This can<br>
be easier to code. Regardless, you'll have to check out the
GLYCAM<br>
documentation and see what is meant, before you can address
how to<br>
convert it into a GROMACS format. Obviously the contents of
parts of<br>
chapter 4 and 5 of the manual will be important.<br>
<br>
<br>
<br>
Mark<br>
<br>
<br>
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