Re: [gmx-users] force filed parameters for phosphoserine with gromaces

2016-06-02 Thread Justin Lemkul 



On 6/2/16 9:59 PM, YanhuaOuyang wrote:

What you mean is that I can use the AMBER parameters on the website 
(http://sites.pharmacy.manchester.ac.uk/bryce/amber 
) and need to convert the 
format of the parameters to the one that GROMACS is compatible with in the .rtp 
entries?


Yes.

-Justin


在 2016年6月3日，上午5:50，Justin Lemkul  写道：



On 6/2/16 10:55 AM, YanhuaOuyang wrote:

Dear Gromacs users,

I am going to run a MD of a 20-residue protein which is phosphorylated on the
Serine and Threonine residues with AMBER ff99SB-ILDN force field using
Gromacs5.0. When I run gmx pdb2gmx and choose AMBER ff99SB-ILDN force field,
it appears: fatal error: residues SEP not found in residue topology
database.

I search some papers, and they say that we need to add add force fields
parameters for the phosphorylated amino acids to the force filed parameter
files. But I do not know how to add force fields parameters for the
phosphorylated amino acids. Could anyone knows how to construct a model for
the phosphorylated protein?



AMBER parameters are already available:

http://sites.pharmacy.manchester.ac.uk/bryce/amber

You just need to convert the format and build suitable .rtp entries.  Or find a 
force field that already has this done for you (CHARMM36, Gromos96 43a1p, etc).

-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

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

==
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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

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

==
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Re: [gmx-users] force filed parameters for phosphoserine with gromaces

2016-06-02 Thread YanhuaOuyang 
What you mean is that I can use the AMBER parameters on the website 
(http://sites.pharmacy.manchester.ac.uk/bryce/amber 
) and need to convert the 
format of the parameters to the one that GROMACS is compatible with in the .rtp 
entries? 
> 在 2016年6月3日，上午5:50，Justin Lemkul  写道：
> 
> 
> 
> On 6/2/16 10:55 AM, YanhuaOuyang wrote:
>> Dear Gromacs users,
>> 
>> I am going to run a MD of a 20-residue protein which is phosphorylated on the
>> Serine and Threonine residues with AMBER ff99SB-ILDN force field using
>> Gromacs5.0. When I run gmx pdb2gmx and choose AMBER ff99SB-ILDN force field,
>> it appears: fatal error: residues SEP not found in residue topology
>> database.
>> 
>> I search some papers, and they say that we need to add add force fields
>> parameters for the phosphorylated amino acids to the force filed parameter
>> files. But I do not know how to add force fields parameters for the
>> phosphorylated amino acids. Could anyone knows how to construct a model for
>> the phosphorylated protein?
>> 
> 
> AMBER parameters are already available:
> 
> http://sites.pharmacy.manchester.ac.uk/bryce/amber
> 
> You just need to convert the format and build suitable .rtp entries.  Or find 
> a force field that already has this done for you (CHARMM36, Gromos96 43a1p, 
> etc).
> 
> -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
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> 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 send a 
> mail to gmx-users-requ...@gromacs.org.

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Re: [gmx-users] force filed parameters for phosphoserine with gromaces

2016-06-02 Thread Justin Lemkul 



On 6/2/16 10:55 AM, YanhuaOuyang wrote:

Dear Gromacs users,

I am going to run a MD of a 20-residue protein which is phosphorylated on the
Serine and Threonine residues with AMBER ff99SB-ILDN force field using
Gromacs5.0. When I run gmx pdb2gmx and choose AMBER ff99SB-ILDN force field,
it appears: fatal error: residues SEP not found in residue topology
database.

I search some papers, and they say that we need to add add force fields
parameters for the phosphorylated amino acids to the force filed parameter
files. But I do not know how to add force fields parameters for the
phosphorylated amino acids. Could anyone knows how to construct a model for
the phosphorylated protein?



AMBER parameters are already available:

http://sites.pharmacy.manchester.ac.uk/bryce/amber

You just need to convert the format and build suitable .rtp entries.  Or find a 
force field that already has this done for you (CHARMM36, Gromos96 43a1p, etc).


-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

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

==
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Gromacs Users mailing list

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[gmx-users] force filed parameters for phosphoserine with gromaces

2016-06-02 Thread YanhuaOuyang 
Dear Gromacs users,

I am going to run a MD of a 20-residue protein which is phosphorylated on the 
Serine and Threonine residues with AMBER ff99SB-ILDN force field using  
Gromacs5.0. When I run gmx pdb2gmx and choose AMBER ff99SB-ILDN force field, it 
appears:
fatal error: residues SEP not found in residue topology database.

I search some papers, and they say that we need to add add force fields 
parameters for the phosphorylated amino acids to the force filed parameter 
files. But I do not know how to add force fields parameters for the 
phosphorylated amino acids. Could anyone knows how to construct a model for the 
phosphorylated protein?

Best regards,
Ouyang.
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