Dear all,
I am very new to Gramacs (switching from AMBER in order to use GROMOS and
CHARMM force fields for carbohydrates) and need some help in preparing
topologies. I had a brief look in the tutorials and gromacs force field
files but I could not find any useful information about using GROMOS
On 3/20/15 11:51 AM, mish wrote:
Dear all,
I am very new to Gramacs (switching from AMBER in order to use GROMOS and
CHARMM force fields for carbohydrates) and need some help in preparing
topologies. I had a brief look in the tutorials and gromacs force field
files but I could not find any
On 3/20/15 1:16 PM, Marcelo Depólo wrote:
As my previous email said: there is a modified GROMOS forcefield for
carbohydrated. Install it and check out which kind of modifications on
topologies you should do.
Install it, sure, but from where? You provided a DOI to the article, which
makes
Many thanks :). It should be enough to start.
Best,
Mish
On Fri, Mar 20, 2015 at 6:32 PM, Thomas Piggot t.pig...@soton.ac.uk wrote:
Hi,
You can download the parameters from:
http://dqfnet.ufpe.br/biomat/Software_files/GROMOS-53A6glyc.tar
I have used them and they seem to perform fine.
On 3/20/15 12:30 PM, mish wrote:
Many thanks. I know parameters are available in literature but my question
was how to use them in GROMACS. Now, I can see different residue names
(e.g AMAN, BMAN, AGAL, BGAL etc for different monosaccharides in CHARMM).
I think I will need to edit input pdb
From article to topology would be time taking and also more chances of
mistakes. Carbohydrates are quite important class of biomolecules and they
should be available in usable form somewhere :)
On Fri, Mar 20, 2015 at 6:21 PM, Justin Lemkul jalem...@vt.edu wrote:
On 3/20/15 1:16 PM, Marcelo
2015-03-20 14:21 GMT-03:00 Justin Lemkul jalem...@vt.edu:
On 3/20/15 1:16 PM, Marcelo Depólo wrote:
As my previous email said: there is a modified GROMOS forcefield for
carbohydrated. Install it and check out which kind of modifications on
topologies you should do.
Install it, sure, but
Hi,
You can download the parameters from:
http://dqfnet.ufpe.br/biomat/Software_files/GROMOS-53A6glyc.tar
I have used them and they seem to perform fine. They are not too
different from the previous 45A4/53A6 parameters.
Cheers
Tom
On 20/03/15 17:21, Justin Lemkul wrote:
On 3/20/15
There is also a Modified GROMOS forcefield for glycans here:
http://dx.doi.org/10.1021/ct300479h
Cheers!
--
Marcelo Depólo Polêto
Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil)
--
Gromacs Users mailing list
* Please search the
On 3/20/15 12:46 PM, mish wrote:
Many thanks. Is it possible that GROMOS parameters re also available in
similar format like CHARMM? With GROMACS there is only aminoacids.rtp
provided for recent GROMOS parameters. In general, I see only protein, dna,
rna and lipid parameters are provided in
Many thanks. I know parameters are available in literature but my question
was how to use them in GROMACS. Now, I can see different residue names
(e.g AMAN, BMAN, AGAL, BGAL etc for different monosaccharides in CHARMM).
I think I will need to edit input pdb file accordingly. However, I am still
Many thanks. Is it possible that GROMOS parameters re also available in
similar format like CHARMM? With GROMACS there is only aminoacids.rtp
provided for recent GROMOS parameters. In general, I see only protein, dna,
rna and lipid parameters are provided in code (included in /top directory)
but
As my previous email said: there is a modified GROMOS forcefield for
carbohydrated. Install it and check out which kind of modifications on
topologies you should do.
2015-03-20 13:51 GMT-03:00 Justin Lemkul jalem...@vt.edu:
On 3/20/15 12:46 PM, mish wrote:
Many thanks. Is it possible that
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