[gmx-users] Carbohydrate force fields in GROMACS

Post by mish
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 or
CHARMM force-field for monosaccharides. I would very happy of there are
some tutorial where it is described. I had a deep look in the ff files and
it loooks like parameters for carbohydrates are not included like for
proteins (as it is done for GLYCAM in Amber). Can someone suggest me how to
set-up a simulation of protein monosaccharides (Methyl-Mannose) using
GROMOS and also CHARM. Moreover, what would be the appropriate choice for
protein in both case ? Although, I would like to use AMBER for proteins.

We provide the full CHARMM36 force field, including all the monosaccharides:

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

If you want to construct modified monosaccharides or polysaccharides, you have
to create special residues in the .rtp for pdb2gmx to process them. See
previous discussions on this topic in the archive.

-Justin
--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

***@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================

Marcelo Depólo

2015-03-20 16:00:56 UTC

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)

mish

2015-03-20 16:30:48 UTC

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
not sure of methylated monosaccharides have to be constructed as "modified
monosaccharides", or there are CHARMM parameters for methy (as a separate
residue) available and one should use 2 residues in such case. I will have
a look in archive to find-out how to create modified monosaccharides.

Many thanks,
Mish

Post by Marcelo DepÃ³lo
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)
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Justin Lemkul

2015-03-20 16:36:42 UTC

Post by mish
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

Yes, .rtp and coordinate file residue names must match.

Post by mish
not sure of methylated monosaccharides have to be constructed as "modified
monosaccharides", or there are CHARMM parameters for methy (as a separate
residue) available and one should use 2 residues in such case. I will have
a look in archive to find-out how to create modified monosaccharides.

In CHARMM, there are "patches" that are applied to various residues. There is
limited support for such modifications in GROMACS. You can define .tdb entries,
but those only work for Protein, DNA, and RNA. So you should not define
separate residues for, e.g. a monosaccharide and a methyl "residue." Instead, a
methylated sugar as a single .rtp entry is the foolproof approach. Chapter 5 of
the manual is your friend (.rtp syntax is straightforward) as well as
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin
--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

***@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================

mish

2015-03-20 16:46:45 UTC

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 not for carbohydrates. Do I need to get GROMOS one from literature ?

Yes, .rtp and coordinate file residue names must match.
not sure of methylated monosaccharides have to be constructed as "modified

Post by mish
monosaccharides", or there are CHARMM parameters for methy (as a separate
residue) available and one should use 2 residues in such case. I will have
a look in archive to find-out how to create modified monosaccharides.

In CHARMM, there are "patches" that are applied to various residues.
There is limited support for such modifications in GROMACS. You can define
.tdb entries, but those only work for Protein, DNA, and RNA. So you should
not define separate residues for, e.g. a monosaccharide and a methyl
"residue." Instead, a methylated sugar as a single .rtp entry is the
foolproof approach. Chapter 5 of the manual is your friend (.rtp syntax is
straightforward) as well as http://www.gromacs.org/
Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
http://mackerell.umaryland.edu/~jalemkul
==================================================
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Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/GMX-Users_List before posting!
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Justin Lemkul

2015-03-20 16:51:14 UTC

Post by mish
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 not for carbohydrates. Do I need to get GROMOS one from literature ?

They're included in aminoacids.rtp for every GROMOS force field, but those
parameters likely aren't the latest (since they go back to 43A1), so you'll have
to replace them or create your own force field directory with updated
parameters. Check the user contributions page or the ATB server; they may have
the latest files.

-Justin

Yes, .rtp and coordinate file residue names must match.
not sure of methylated monosaccharides have to be constructed as "modified

In CHARMM, there are "patches" that are applied to various residues.
There is limited support for such modifications in GROMACS. You can define
.tdb entries, but those only work for Protein, DNA, and RNA. So you should
not define separate residues for, e.g. a monosaccharide and a methyl
"residue." Instead, a methylated sugar as a single .rtp entry is the
foolproof approach. Chapter 5 of the manual is your friend (.rtp syntax is
straightforward) as well as http://www.gromacs.org/
Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/GMX-Users_List before posting!
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Marcelo Depólo

2015-03-20 17:16:30 UTC

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.

They're included in aminoacids.rtp for every GROMOS force field, but those
parameters likely aren't the latest (since they go back to 43A1), so you'll
have to replace them or create your own force field directory with updated
parameters. Check the user contributions page or the ATB server; they may
have the latest files.
-Justin

Post by mish
Many thanks. I know parameters are available in literature but my

Post by mish
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

Yes, .rtp and coordinate file residue names must match.
not sure of methylated monosaccharides have to be constructed as "modified

There is limited support for such modifications in GROMACS. You can define
.tdb entries, but those only work for Protein, DNA, and RNA. So you should
not define separate residues for, e.g. a monosaccharide and a methyl
"residue." Instead, a methylated sugar as a single .rtp entry is the
foolproof approach. Chapter 5 of the manual is your friend (.rtp syntax is
straightforward) as well as http://www.gromacs.org/
Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
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--
Marcelo Depólo Polêto
Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil)

Justin Lemkul

2015-03-20 17:21:22 UTC

Post by Marcelo DepÃ³lo
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 no reference to the availability of the parameters. If the implication is
that one needs to manually modify all of the force field files according to what
the authors reported, that's one thing, but if you know of a site from which you
can download the modified force field, that would be helpful. I would be
curious to see how well the parameters perform, as well.

-Justin

They're included in aminoacids.rtp for every GROMOS force field, but those
parameters likely aren't the latest (since they go back to 43A1), so you'll
have to replace them or create your own force field directory with updated
parameters. Check the user contributions page or the ATB server; they may
have the latest files.
-Justin

Post by mish
Many thanks. I know parameters are available in literature but my

Yes, .rtp and coordinate file residue names must match.
not sure of methylated monosaccharides have to be constructed as "modified

mish

2015-03-20 17:32:47 UTC

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 :)

Post by Marcelo DepÃ³lo
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 no reference to the availability of the parameters. If the
implication is that one needs to manually modify all of the force field
files according to what the authors reported, that's one thing, but if you
know of a site from which you can download the modified force field, that
would be helpful. I would be curious to see how well the parameters
perform, as well.
-Justin

Post by mish
Many thanks. Is it possible that GROMOS parameters re also available in

Post by mish
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 not for carbohydrates. Do I need to get GROMOS one from literature ?
They're included in aminoacids.rtp for every GROMOS force field, but

those
parameters likely aren't the latest (since they go back to 43A1), so you'll
have to replace them or create your own force field directory with updated
parameters. Check the user contributions page or the ATB server; they may
have the latest files.
-Justin

Post by mish
Many thanks. I know parameters are available in literature but my

not sure of methylated monosaccharides have to be constructed as "modified
monosaccharides", or there are CHARMM parameters for methy (as a

Post by mish
separate
residue) available and one should use 2 residues in such case. I will have
a look in archive to find-out how to create modified monosaccharides.
In CHARMM, there are "patches" that are applied to various residues.

There is limited support for such modifications in GROMACS. You can define
.tdb entries, but those only work for Protein, DNA, and RNA. So you should
not define separate residues for, e.g. a monosaccharide and a methyl
"residue." Instead, a methylated sugar as a single .rtp entry is the
foolproof approach. Chapter 5 of the manual is your friend (.rtp
syntax
is
straightforward) as well as http://www.gromacs.org/
Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
--

==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
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Support/Mailing_Lists/GMX-Users_List before posting!
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Marcelo Depólo

2015-03-20 17:33:34 UTC

Post by Marcelo DepÃ³lo
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 no reference to the availability of the parameters. If the
implication is that one needs to manually modify all of the force field
files according to what the authors reported, that's one thing, but if you
know of a site from which you can download the modified force field, that
would be helpful.

You can find the forcefield here: http://dqfnet.ufpe.br/biomat/Software.html,
provided by one of leaders of the paper.

I would be curious to see how well the parameters perform, as well.
-Justin

Post by mish
Many thanks. Is it possible that GROMOS parameters re also available in

Post by mish
Many thanks. I know parameters are available in literature but my

not sure of methylated monosaccharides have to be constructed as "modified
monosaccharides", or there are CHARMM parameters for methy (as a

There is limited support for such modifications in GROMACS. You can define
.tdb entries, but those only work for Protein, DNA, and RNA. So you should
not define separate residues for, e.g. a monosaccharide and a methyl
"residue." Instead, a methylated sugar as a single .rtp entry is the
foolproof approach. Chapter 5 of the manual is your friend (.rtp
syntax
is
straightforward) as well as http://www.gromacs.org/
Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
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--

--
Marcelo Depólo Polêto
Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil)

Thomas Piggot

2015-03-20 17:32:10 UTC

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

Post by Marcelo DepÃ³lo
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 no reference to the availability of the parameters. If
the implication is that one needs to manually modify all of the force
field files according to what the authors reported, that's one thing,
but if you know of a site from which you can download the modified
force field, that would be helpful. I would be curious to see how well
the parameters perform, as well.
-Justin

Post by mish
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 not for carbohydrates. Do I need to get GROMOS one from
literature ?

They're included in aminoacids.rtp for every GROMOS force field, but those
parameters likely aren't the latest (since they go back to 43A1), so you'll
have to replace them or create your own force field directory with updated
parameters. Check the user contributions page or the ATB server; they may
have the latest files.
-Justin

Post by mish
Many thanks. I know parameters are available in literature but my

Yes, .rtp and coordinate file residue names must match.
not sure of methylated monosaccharides have to be constructed as "modified

Post by mish
monosaccharides", or there are CHARMM parameters for methy (as a separate
residue) available and one should use 2 residues in such case. I
will
have
a look in archive to find-out how to create modified
monosaccharides.
In CHARMM, there are "patches" that are applied to various residues.

There is limited support for such modifications in GROMACS. You can define
.tdb entries, but those only work for Protein, DNA, and RNA. So you should
not define separate residues for, e.g. a monosaccharide and a methyl
"residue." Instead, a methylated sugar as a single .rtp entry is the
foolproof approach. Chapter 5 of the manual is your friend (.rtp
syntax
is
straightforward) as well as http://www.gromacs.org/
Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
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--
Dr Thomas Piggot
University of Southampton, UK.

mish

2015-03-20 17:41:04 UTC

Many thanks :). It should be enough to start.

Best,
Mish

Post by Thomas Piggot
Hi,
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

Post by Marcelo DepÃ³lo
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 no reference to the availability of the parameters. If the
implication is that one needs to manually modify all of the force field
files according to what the authors reported, that's one thing, but if you
know of a site from which you can download the modified force field, that
would be helpful. I would be curious to see how well the parameters
perform, as well.
-Justin

Post by mish
Many thanks. Is it possible that GROMOS parameters re also available in