Hi Ahbisek,
Thanks for trying this solution. I just noticed that you are using "&wt type='RAMP'", where RAMP is not a valid varying condition listed in chapter 22.9 of the AmberTools25 manual.
Could you kindly share which tutorial you are following? I don't think I have encountered the variables "ivar" and "ifvar" before either.
Thank you!
Zhen.
_____________________
Zhen Li<
http://lizhen62017.wixsite.com/home>, Ph.D.,
The Merz Research Group<
http://merzgroup.org>,
Michigan State University,
Cleveland Clinic.
________________________________
From: Abhisek Jana <20004055.iitb.ac.in>
Sent: Tuesday, October 28, 2025 12:47 AM
To: Li, Zhen <lizhen6.chemistry.msu.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Assistance with SMD Error Related to Hydrogen Bond Collective Variables
Hi Zhen,
Thanks for your valuable suggestion. I changed the smd.in and disang.in as you mentioned.
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,
/
# --- 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
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 /
Now the output files stop before starting the SMD. The output is given below:
| Conditional Compilation Defines Used:
| PUBFFT
| BINTRAJ
| CUDA
| EMIL
| Largest sphere to fit in unit cell has radius = 45.831
| New format PARM file being parsed.
| Version = 1.000 Date = 08/08/25 Time = 18:49:53
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting box info from netcdf restart file
NATOM = 109569 NTYPES = 22 NBONH = 101939 MBONA = 7649
NTHETH = 16141 MTHETA = 10514 NPHIH = 32966 MPHIA = 31743
NHPARM = 0 NPARM = 0 NNB = 206998 NRES = 32709
NBONA = 7649 NTHETA = 10514 NPHIA = 31743 NUMBND = 114
NUMANG = 261 NPTRA = 245 NATYP = 51 NPHB = 1
IFBOX = 2 NMXRS = 34 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Can you please check the output and give suggestions?
Thanks,
Abhisek Jana
Department of Chemistry
IIT Bombay
On 2025-10-27 18:53, Li, Zhen via AMBER wrote:
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<
https://urldefense.com/v3/__http://lizhen62017.wixsite.com/home__;!!HXCxUKc!w1reSH5NTaxEZeQE63Hi_cOx8jp8BdsWezY6XKeMTDGiC8_nRDJIGepqiHU-YYzQC-ZZNZXezQOLbt4v-4951jQH2W8$>>, Ph.D.,
The Merz Research Group<
http://merzgroup.org<
https://urldefense.com/v3/__http://merzgroup.org__;!!HXCxUKc!w1reSH5NTaxEZeQE63Hi_cOx8jp8BdsWezY6XKeMTDGiC8_nRDJIGepqiHU-YYzQC-ZZNZXezQOLbt4v-4952YcazsY$>>,
Michigan State University,
Cleveland Clinic.
________________________________
From: Abhisek Jana via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>>
Sent: Monday, October 27, 2025 1:33 AM
To: amber.ambermd.org<mailto:amber.ambermd.org> <amber.ambermd.org<mailto: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 Tue Oct 28 2025 - 08:00:03 PDT
