- The original force field: amber14sb_parmbsc1.ff.tar.gz by mhviet, 2017
- CUFIX corrections by Yoo & Aksimentiev, 2018
All the manipulations were carried out according to Yoo & Aksimetiev group website. Here is what was done:
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Downloaded package https://www.dropbox.com/sh/90quvm5sla7oqym/AAABoTI9-Z4aLnm-QxDVm_o5a?dl=0
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Copied these files to the original .ff file: cufix.itp, mg-sol6.itp, mg-sol6.pdb, ca-sol7.itp, ca-sol7.pdb.
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Replaced atom types for O1P and O2P atoms (O2) with ON2 for all nucleotides in dna.rtp and rna.rtp. ON2 atom type is defined in cufix.itp.
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It is not stated in the instructionb on the Aksiemetiev website. You should add atomtypes in cufix.itp:
NH3 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 ;jejoong spermine
NP 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 ;jejoong spermine
- Added
#include "cufix.itp"to forcefield.itp between#include "ffnonbonded.itp"and#include "ffbonded.it". - Deleted the following ions from ffnonbonded.itp: Li, Na, K, Cl, MG, Rb, Cs, F, Br, I. CUFIX uses new ion parameters by the Cheatham group.