Dear all,
I am using AmberTools 16 to assign charges to my molecules and to fit missing parameters for the GAFF using parmchk2. Parmchk gives the following output:
Remark line goes here
MASS
BOND
ANGLE
DIHE
os-c3-cx-cx 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 92.0
os-c3-cx-os 1 0.144 0.000 -3.000 same as os-c3-c3-os
os-c3-cx-os 1 1.175 0.000 2.000 same as os-c3-c3-os, penalty score= 92.0
os-c3-cx-h1 1 0.000 0.000 -3.000 same as h1-c3-c3-os
os-c3-cx-h1 1 0.250 0.000 1.000 same as h1-c3-c3-os, penalty score= 92.0
c3-cx-os-cx 1 0.383 0.000 -3.000 same as c3-c3-os-c3
c3-cx-os-cx 1 0.100 180.000 2.000 same as c3-c3-os-c3, penalty score=179.0
cx-cx-os-cx 1 0.383 0.000 -3.000 same as c3-c3-os-c3
cx-cx-os-cx 1 0.100 180.000 2.000 same as c3-c3-os-c3, penalty score=266.0
h1-cx-os-cx 3 1.150 0.000 3.000 same as X -c3-os-X , penalty score= 92.0
h1-c3-cx-cx 1 0.160 0.000 3.000 same as hc-c3-c3-c3, penalty score=266.0
h1-c3-cx-os 1 0.000 0.000 -3.000 same as h1-c3-c3-os
h1-c3-cx-os 1 0.250 0.000 1.000 same as h1-c3-c3-os, penalty score= 92.0
h1-c3-cx-h1 1 0.150 0.000 3.000 same as hc-c3-c3-hc, penalty score=266.0
IMPROPER
ca-ca-ca-os 1.1 180.0 2.0 Using the default value
ca-ca-ca-ha 1.1 180.0 2.0 Using general improper torsional angle X- X-ca-ha, penalty score= 6.0)
NONBON
My questions are the following:
1) Why are in some cases two parameters given for the same dihedral?
2) Can the general dihedrals (e.g X-c3-c3-X) be used in all dihedrals following the type or should I follow the parmchk suggestions?
3) How can I recalculate parameters for dihedrals using the atomic charges calculated with Antechamber?
Thank you very much in advance and I wish to all a great day.
Andreas Gavrielides
Doctorant au CIRIMAT-INP Toulouse
SURF Equipe
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Received on Tue Dec 06 2016 - 02:30:02 PST
