Rasoul wrote:
On Thu, Aug 19, 2010 at 1:02 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Rasoul wrote:
For the sugar parameters you can use Glycam parameters
http://glycam.ccrc.uga.edu/documents/gl_params.jsp
After with specific script it can be convert to Gromac readable
file:
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software
Mixing and matching force field parameters is a very bad idea. To
have a valid
physical model, parameters should be derived in compatible ways.
It has good consistency with Amber FF :J Comput Chem 29: 622–655, 2008.
That's exactly what it was designed to do, which I don't question. But the OP
was attempting to develop united-atom parameters for use with Gromos96 53A6.
For clarity, I pointed out that mixing GLYCAM and 53A6 is an incorrect notion.
-Justin
-Justin
Rasoul
I hope it would be useful for you.
Rasoul
On Wed, Aug 18, 2010 at 6:45 PM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
Jianhui Tian wrote:
Hi Parichita,
Thanks for the suggestion. However, the question is what
parameters from ffG53a6 can be used for not included
sugars or
glycolipid. I guess you can not simply use the charge,
angle and
dihedral values based on the atom types from 53a6.
Gromos building blocks are quite transferable between different
molecules. Compare a few sugars - the parameters are nearly
identical. That is one of the central features of this
particular
force field, that functional group charges should be as
versatile as
possible.
As for the lipids, there are new versions of 53A6 (which I
believe
have been uploaded to the Gromacs site) that perform
substantially
better than the built-in parameters. The long acyl chains
are not
particularly accurate in the default 53A6.
-Justin
Jianhui
Date: Wed, 18 Aug 2010 16:18:49 +0530 (IST)
From: parichita parichita <[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>
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>
Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6
To: Discussion list for GROMACS users
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<mailto:[email protected]>> <mailto:[email protected]
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Hi Jianhui,
For your sugar part you can use PRODRG, which will convert
coordinates for small molecules in PDB format (or simple text
structures) to the following topology formats: GROMOS,
GROMACS
and from literature if you can find out the parameters of
ffG53a6 force field, then you can correct the charge,
angle and
dihedral values that you are collected from the PRODRG. Hope
this will help you.
Regards...
Parichita...........
Parichita Mazumder Research Fellow
C/O Dr. Chaitali Mukhopadhayay
Department of Chemistry
University of Calcutta
92,A P C Road
Kolkata-700009
India.
--- On Wed, 18/8/10, Jianhui Tian <[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>> <mailto:[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>>> wrote:
From: Jianhui Tian <[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>> <mailto:[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>>>
Subject: [gmx-users] carbohydrate parameters in ffG53a6
To: [email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
<mailto:[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>>
Date: Wednesday, 18 August, 2010, 10:16 AM
Hi,
I want to do some simulations about carbohydrates and
glycolipid. In the ffG53a6.rtp file, I just see limited
parameters for carbohydrate, like monosaccharide Glucose,
Mannose and Galactose. What parameters can be used for others
like arabinose? Also, is there any parameters available
in the
Gromacs force field for glycolipid?
Jianhui
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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