On 20/07/2011 7:33 PM, sa wrote:
Thank you Austin, for the clarification,
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.
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.
Mark
Thank you again for your advice.
SA-
Message: 1
Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT)
From: "Austin B. Yongye" <ybau...@yahoo.com
<mailto:ybau...@yahoo.com>>
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
in the GROMACS format.
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
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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:
O2-P
-OS-CP 1 0.10 0.0 -3.
Dimethyl phosphate
1 -0.50 0.0 -2.
1 0.10
0.0 1
-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.
Hope that helps.
Austin-
--- On Tue, 7/19/11, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
From: Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral
parameters in the GROMACS format.
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Date: Tuesday, July 19, 2011, 7:08 AM
On 19/07/2011 11:56 PM, sa wrote:
Dear
GROMCS users,
I
am trying to convert some GLYCAM parameters in GROMACS
format.
For this
purpose, I am using the latest GLYCAM parameters downloaded
from the RJ. Woods'
website and the examples given in the acpype code (here for
the dihedral angles) :
http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9&r=9&redir=1
<http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9&r=9&redir=1>
-------------------
# dihedral idivf barrier hight/2 kcal/mol phase degrees
periodicity comments
X -ca-ca-X 4 14.500*
180.000 2.000 intrpol.bsd.on C6H6
* to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in
topolbuild, why?) = 30.334 or 15.167 kJ/mol
# X -CA-CA-X 4 14.50 180.0 2.
intrpol.bsd.on C6H6 (from parm99.dat)
# X-CA-CA-X 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ; intrpol.bsd.on C6H6
-----------
I have no problems with the parameters for proteins. But, in
case of the GLYCAM parameters, I am a little confused
about the conversion of dihedral force constants (DFC), especially
when the DFC and the periodicity values are < 0 for example
for this torsion:
O2-P
-OS-CP 1 0.10 0.0 -3.
Dimethyl phosphate
1 -0.50 0.0 -2.
1 0.10
0.0 1
Where only a positive value makes sense, sometimes people use
negative values to indicate some special functional form. This can
be easier to code. Regardless, you'll have to check out the GLYCAM
documentation and see what is meant, before you can address how to
convert it into a GROMACS format. Obviously the contents of
parts of
chapter 4 and 5 of the manual will be important.
Mark
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