You need a comma after every variable definition (missing after ntmin=0)
On Sat, Feb 21, 2026, 3:39 AM Mandar Kulkarni via AMBER <amber.ambermd.org>
wrote:
> ARES PRIVATE
>
> My email address is now .a-star.edu.sg. Kindly update your address book
> accordingly.
>
> 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 - 04:30:03 PST
