Hello,
I am using AMBER22 to calculate the NMR conformation of the G-quadruplex using restraints for the 1st time. I am using the protocol from amber 22 help. 9.1 NMR Refinement of DNA and RNA Duplexes<
https://ambermd.org/tutorials/advanced/tutorial4/index.php>. I am using the following script for SA.
#simulated annealing protocol, 800 ps, amber
&cntrl
nstlim=200000,
dt=0.0004
ntc=2,
ntpr=2000,
ntwx=2000,
ntb=0,
igb=2,
ntt=3,
gamma_ln=2.0,
tempi=300,
temp0=300.0,
cut=10000
nmropt=1,
ntxo=1,
/
&wt type='TEMP0', istep1=0,istep2=5000, value1=0.0, value2=300.0, /
&wt type='TEMP0', istep1=5001,istep2=100000, value1=300.0, value2=700.0, /
&wt type='TEMP0', istep1=100001,istep2=150000, value1=700.0, value2=1000.0, /
&wt type='TEMP0', istep1=150001,istep2=200000, value1=1000.0, value2=0.0, /
&wt type='END',
/
LISTOUT=POUT
DISANG=NOESY.rst
#
However, it is not clear to me where to modify to calculate the 100 conformations and select the best 10/20 best on final energies. Please help me to change the script.
Best Regards,
Anirban
Ph.D . Anirban Ghosh | CEITEC MU
Postdoctoral Fellow
Web: www.ceitec.eu<http://www.ceitec.eu/>
https://www.ceitec.eu/non-coding-genome-lukas-trantirek/rg109
Masaryk University
CEITEC - Central European Institute of Technology
Kamenice 5, 625 00 Brno, Czech Republic
Office no. A35/ASO22
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Received on Sun Feb 12 2023 - 12:30:02 PST
