[gmx-users] how can we modify *.rtp file (again again)

Mark Abraham mark.j.abraham at gmail.com
Thu Jan 22 16:51:07 CET 2015


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>    1.
>    Since we created covalent bond between glucose and insulin, Should we
>    consider Glucose as a reagent in residuetype.dat?

Doesn't matter unless you care about how default groups like "Protein" are
interpreted, e.g. for use with temperature-coupling groups.

>    2.
>    In the ffbonded.itp, Are CA and CHn same components?
>    3.
>    Do the bonds between C-O (single or double bond) include in gb_4?
>    4.
>    What's the meaning of OA and OM?

Some of these are covered in atomtypes.atp. Other clues may be in the
original literature for your force field, or how the interactions are used
in other .rtp entries.


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