ARES PRIVATE
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Dear Amber Community,
I am calculating MM energy with sander for conformers of modified nucleoside
I am following a protocol by Yildirim et al. (J. Chem. Theory Comput., Vol. 6, No. 5, 2010) for-MM energy calculation. I am not well-acquainted with overall Amber scripts and still exploring.
I am currently using following sander input for minimization; I tried to put scee = 1.2 and scnb = 2.0 parameters for 1-4 screening but run fails. Is there any way to calculate MM energy with screening factors included?
EM with minimization
&cntrl
imin=1, ! energy minimization
maxcyc=1000, ! max cycles
ntmin = 0 ! Full conjugate gradient minimization
nmropt=1, ! NMR-like restraints for dihedral
ntpr = 10, ! print energy information every 10 steps
ntb = 0, ! zero periodicty and PME is off
cut = 999.00, ! effectively infinite cutoff
/
&wt type='END'
/
DISANG=dihedral.rst
sander -O -i mdin_2 -o mdout -p res_PSUN_zerodih.prmtop -c res_PSUN.inpcrd
Also,
I am generating new topology res_PSUN_zerodih.prmtop with original prmtop and zero_kappa.frcmod with tleap.
Zero_kappa.frcmod is as follows:
DIHE
OS-CT-CM-C 1 0.000 0.000 0.000
OS-CT-CM-CM 1 0.000 0.000 0.000
Is there any way to set dihedral zero with index or atom names ?
Thanks in advance,
Mandar
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Received on Sat Feb 21 2026 - 04:00:02 PST
