[gmx-users] Adding ADP parameters to GROMACS amber99sb-ildn ff

Robert König olaf2745 at yahoo.de
Sat Feb 17 21:10:15 CET 2018

Dear gmx-users,
because using acpype with the GAFF ff to prepare the topology of ADP leads to unphysical behavior of ADP, in most simulations (even with the correction of https://code.google.com/archive/p/acpype/wikis/FAQ.wiki), I now want to add the ADP parameters from http://research.bmh.manchester.ac.uk/bryce/amber (namely http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/ADP.prep and http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/frcmod.phos) directly to the amber99sb-ildn ff.
That already worked well with SEP and TPO parameters, but here at some points I don't know how to proceed.
There are two points.First http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/ADP.prep these parameters at alland second the "DIHE" parameters from http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/frcmod.phos.

I would be very glad and thankful if someone could help in detail how to implement these two parts properly.
Thank you very much!Sincerly,olaf

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