ARES PRIVATE
My email address is now .a-star.edu.sg. Kindly update your address book accordingly.
Thanks for your reply, getting namelist error after adding missing comma and scee=1.2,scnb=2.0, entries.
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
scee=1.2,scnb=2.0,
/
&wt type='END',
/
DISANG=dihedral.rst
error in reading namelist cntrl
From: Carlos Simmerling <carlos.simmerling.stonybrook.edu>
Date: Saturday, 21 February 2026 at 8:23 PM
To: Mandar Kulkarni <mandar_kulkarni.a-star.edu.sg>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] MM energy with certain zero torsion parameters
CAUTION:
External email. Exercise caution with links and attachments.
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<mailto:amber.ambermd.org>> wrote:
ARES PRIVATE
My email address is now .a-star.edu.sg<
http://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 - 05:00:03 PST
