Hi Abhishek,
To my understanding, you need to do the two changes:
1.
Rewrite the &wt block as
# --- Control time-dependent behavior
&wt type='DUMPFREQ', istep1=500 /
&wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
ivar=1 /
&wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
ivar=2 /
&wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
ivar=3 /
&wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
ivar=4 /
&wt type='END' /
&end
2.
Move the &wt block from disang.in to smd.in (between lines "/" and "DISANG=disang.in"), so disang.in only has the &rst block.
Please let me know whether this modification solved the issue.
Best regards,
Zhen.
1.
_____________________
Zhen Li<
http://lizhen62017.wixsite.com/home>, Ph.D.,
The Merz Research Group<
http://merzgroup.org>,
Michigan State University,
Cleveland Clinic.
________________________________
From: Abhisek Jana via AMBER <amber.ambermd.org>
Sent: Monday, October 27, 2025 1:33 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Assistance with SMD Error Related to Hydrogen Bond Collective Variables
Dear all,
I am performing a steered molecular dynamics (SMD) simulation using
hydrogen bond collective variables defined in the disang.in file.
However, I am encountering the following error:
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 103200.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
ERROR: No "wt" namelist with TYPE=END found
I have attached the smd.in
and disang.in files for your reference. I would greatly appreciate your
feedback and suggestions on the possible cause of this error and how to
resolve it.
smd.in
&cntrl
imin=0, irest=1, ntx=5,
nstlim=500000, dt=0.002,
ntc=2, ntf=2, temp0=300.0,
ntpr=500, ntwx=500, ntwr=5000,
cut=10.0,
nmropt=1,
/
DISANG=disang.in
DUMPAVE=mdpull.dat
disang.in
# disang.in--Time-dependent restraints for SMD pulling of 3 H-bonds
# --- Define the restrained atom pairs (Donor-Acceptor)
&rst iat=14468,13467, rk2=5.0, rk3=5.0, r1=0, r2=2.5, r3=2.5, r4=10.0,
ir6=1, ifvar=1 /
&rst iat=14448,13473, rk2=5.0, rk3=5.0, r1=0, r2=2.5, r3=2.5, r4=10.0,
ir6=1, ifvar=2 /
&rst iat=14423,13512, rk2=5.0, rk3=5.0, r1=0, r2=2.5, r3=2.5, r4=10.0,
ir6=1, ifvar=3 /
&rst iat=14429,13492, rk2=5.0, rk3=5.0, r1=0, r2=2.5, r3=2.5, r4=10.0,
ir6=1, ifvar=4 /
# --- Control time-dependent behavior
&wt type='DUMPFREQ', istep1=500 /
&wt type='END' /
&wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
ivar=1 /
&wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
ivar=2 /
&wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
ivar=3 /
&wt type='RAMP', istep1=0, istep2=500000, value1=2.5, value2=10.0,
ivar=4 /
&end
Best regards,
Abhisek Jana
Institute Postdoctoral Fellow
Department of Chemistry, IIT Bombay
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Received on Mon Oct 27 2025 - 06:30:03 PDT
