[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 <marlon.sidore at gmail.com> 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 <mark.j.abraham at gmail.com>:
> 
>> 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 <15901283893 at 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-request at gromacs.org.
>>> 
>> --
>> 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-request at gromacs.org.
>> 
> -- 
> 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-request at gromacs.org.