Re: [gmx-users] converting the frcmod file and off file to gromacs

[OuyangYanhua]

Thank you for your helpful example.
> 在 2016年6月20日，下午11:17，Marlon Sidore  写道：
> 
> Hi,
> 
> What you want is to convert these from amber (kcal) to gromacs (kJ). I
> followed successfully another post from the mailing list here:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-September/101115.html
> 
> What you should do is make sure your conversion is right, by taking an
> example from the amber forcefield in amber format and its equivalent in
> gromacs format, before applying that conversion on your new parameters.
> 
> Hope that helps.
> 
> Marlon Sidore
> 
> 
> PhD Student
> Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
> CNRS - UMR7255
> 31, Chemin Joseph Aiguier
> 13402 cedex 20 Marseille
> France
> 
> 
> 2016-06-20 16:22 GMT+02:00 Mark Abraham :
> 
>> Hi,
>> 
>> It sounds like what you want to look for is the documentation for those
>> file formats.
>> 
>> Mark
>> 
>> On Sun, 19 Jun 2016 10:05 OuyangYanhua <15901283...@163.com> wrote:
>> 
>>> Hi,
>>> I am simulating a protein phosphorylated on Ser and Thr residues using
>>> AMBER99SB-ILDN ff with Gromacs 5.0. I read the paper that I can use the
>>> phophorylation parameters in the
>>> http://sites.pharmacy.manchester.ac.uk/bryce/amber <
>>> http://sites.pharmacy.manchester.ac.uk/bryce/amber> . However it is
>>> difficult for me to read the parameters and statistics in the frcmod and
>>> off files. So I have trouble in converting the statistics in framod files
>>> and off file to gromacs files, such as .rtp, ffbond.itp.
>>> 
>>> Best regards,
>>> Ouyang
>>> --
>>> 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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>>> 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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>> 
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Re: [gmx-users] converting the frcmod file and off file to gromacs

[OuyangYanhua]

Thank you for your recommend.
> 在 2016年6月20日，下午10:22，Mark Abraham  写道：
> 
> Hi,
> 
> It sounds like what you want to look for is the documentation for those
> file formats.
> 
> Mark
> 
> On Sun, 19 Jun 2016 10:05 OuyangYanhua <15901283...@163.com> wrote:
> 
>> Hi,
>> I am simulating a protein phosphorylated on Ser and Thr residues using
>> AMBER99SB-ILDN ff with Gromacs 5.0. I read the paper that I can use the
>> phophorylation parameters in the
>> http://sites.pharmacy.manchester.ac.uk/bryce/amber <
>> http://sites.pharmacy.manchester.ac.uk/bryce/amber> . However it is
>> difficult for me to read the parameters and statistics in the frcmod and
>> off files. So I have trouble in converting the statistics in framod files
>> and off file to gromacs files, such as .rtp, ffbond.itp.
>> 
>> Best regards,
>> Ouyang
>> --
>> 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] converting the frcmod file and off file to gromacs

[Marlon Sidore]

Hi,

What you want is to convert these from amber (kcal) to gromacs (kJ). I
followed successfully another post from the mailing list here:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-September/101115.html

What you should do is make sure your conversion is right, by taking an
example from the amber forcefield in amber format and its equivalent in
gromacs format, before applying that conversion on your new parameters.

Hope that helps.

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2016-06-20 16:22 GMT+02:00 Mark Abraham :

> Hi,
>
> It sounds like what you want to look for is the documentation for those
> file formats.
>
> Mark
>
> On Sun, 19 Jun 2016 10:05 OuyangYanhua <15901283...@163.com> wrote:
>
> > Hi,
> > I am simulating a protein phosphorylated on Ser and Thr residues using
> > AMBER99SB-ILDN ff with Gromacs 5.0. I read the paper that I can use the
> > phophorylation parameters in the
> > http://sites.pharmacy.manchester.ac.uk/bryce/amber <
> > http://sites.pharmacy.manchester.ac.uk/bryce/amber> . However it is
> > difficult for me to read the parameters and statistics in the frcmod and
> > off files. So I have trouble in converting the statistics in framod files
> > and off file to gromacs files, such as .rtp, ffbond.itp.
> >
> > Best regards,
> > Ouyang
> > --
> > 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.
> >
> --
> 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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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] converting the frcmod file and off file to gromacs

[Mark Abraham]

Hi,

It sounds like what you want to look for is the documentation for those
file formats.

Mark

On Sun, 19 Jun 2016 10:05 OuyangYanhua <15901283...@163.com> wrote:

> Hi,
> I am simulating a protein phosphorylated on Ser and Thr residues using
> AMBER99SB-ILDN ff with Gromacs 5.0. I read the paper that I can use the
> phophorylation parameters in the
> http://sites.pharmacy.manchester.ac.uk/bryce/amber <
> http://sites.pharmacy.manchester.ac.uk/bryce/amber> . However it is
> difficult for me to read the parameters and statistics in the frcmod and
> off files. So I have trouble in converting the statistics in framod files
> and off file to gromacs files, such as .rtp, ffbond.itp.
>
> Best regards,
> Ouyang
> --
> 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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[gmx-users] converting the frcmod file and off file to gromacs

[OuyangYanhua]

Hi,
I am simulating a protein phosphorylated on Ser and Thr residues using 
AMBER99SB-ILDN ff with Gromacs 5.0. I read the paper that I can use the 
phophorylation parameters in the 
http://sites.pharmacy.manchester.ac.uk/bryce/amber 
 . However it is difficult 
for me to read the parameters and statistics in the frcmod and off files. So I 
have trouble in converting the statistics in framod files and off file to 
gromacs files, such as .rtp, ffbond.itp.

Best regards,
Ouyang
-- 
Gromacs Users mailing list

* Please search the archive at 
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