> So my questions are: how to convert it in the gromacs format ?
I haven't done AMBER to GROMACS conversions. But a google search led me to this
page. It's just a matter of knowing the different formats.
http://ffamber.cnsm.csulb.edu
> 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.
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.
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>
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
in the GROMACS format.
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<1311098935.93905.yahoomailclas...@web161426.mail.bf1.yahoo.com>
Content-Type: text/plain; charset="utf-8"
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> wrote:
From: Mark Abraham <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>
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
-------------------
# 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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