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]>
>
Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected]
<mailto:[email protected]>>
Content-Type: text/plain; charset="iso-8859-1"
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]>> wrote:
From: Jianhui Tian <[email protected] <mailto:[email protected]>>
Subject: [gmx-users] carbohydrate parameters in ffG53a6
To: [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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
