Dear Amber users,
I am trying to run simulations in Amber20 using Amoeba Force Field, but I faced some problems. I have tried 3 different tutorials, but all of them end with the same notification and empty prmtop and incrd files.
For example, I have done this:
tleap
source leaprc.ff14SB
gag = sequence { NGLY ALA CGLY }
solvatebox gag TIP3PBOX 6.5 iso
saveamberparm gag amberfc.prmtop amberfc.inpcrd
savepdb gag gag_wat.pdb
quit
Then I created gag_wat.key which is:
parameters /home/klyuchnikov/Tinker-FFE/ffe/../tinker/params/amoebapro13
a-axis 30.1341540
b-axis 30.5110950
c-axis 30.2224290
Then I created tinker XYZ file:
pdbxyz gag_wat
and analout file:
analyze gag_wat PC > gag_wat.analout
And after using tinker_to_amber:
tinker_to_amber -name gag_wat -title “GAG peptide AMOEBA ff”
I have got this output
frcfieldfile = /home/klyuchnikov/Tinker-FFE/ffe/../tinker/params/amoebapro13.prm
found a-axis = 30.134153999999999
found b-axis = 30.511095000000001
found c-axis = 30.222429000000002
num_xyz_atoms = 1704
numres = 562
num_atoms = 1704
no success getting Atom Type Definition Parameters
and both prmtop and incrd files are empty.
Can you help me to figure out what is the possible reason for this problem?
Thank you in advance,
Evgenii
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Received on Fri Jul 17 2020 - 13:00:02 PDT
