I guess this line in your output is key:
WARNING: Local coordinate 1 differs from partner coordinate 1 !
In your system. all atoms that are not modified in the TI run should start
with identical input XYZ coordinates. Since this is not true for your first
atom, probably your entire system is shifted between the lambda values, or
the atom ordering is different.
You should check and adjust these atom coordinates, the simplest way could
just be by ambpdb'ing your input files and comparing side by side in a text
editor.
Kind Regards,
Thomas
On Tue, Aug 13, 2024 at 11:19 PM Weerawarna Kurukulasooriy, Sandaruwani
Tharaka [CHEM] via AMBER <amber.ambermd.org> wrote:
> **Warning** The sender address ("Weerawarna Kurukulasooriy, Sandaruwani
> Tharaka \[CHEM\] via AMBER" ) can not be verified, sender email address
> could be spoofed. Please take care to proceed.
> Hi,
>
> Thank you for the help. I turned off the positional restraints. But now I
> am getting the below error. Can someone please help me with this?
>
> Kind Regards
> Sandaruwani
>
>
> -------------------------------------------------------
> Amber 21 SANDER 2021
> -------------------------------------------------------
>
> | Run on 08/12/2024 at 19:53:33
>
> | Executable path:
> /global/common/software/nersc/pm-2021q4/sw/amber/20/bin/sander.MPI
> | Working directory: /pscratch/sd/s/sandaru/TI/new
> | Hostname: nid006162
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: mdin_min_v0_l0.02
> | MDOUT: Nd_IL3_min_v0_l0.02.out
> |INPCRD: Nd_IL3_0.rst
> | PARM: Nd_IL3.prmtop
> |RESTRT: Nd_IL3_min_v0_l0.02.rst
> | REFC: Nd_IL3_0.rst
> | MDVEL: mdvel.000
> | MDFRC: mdfrc.000
> | MDEN: mden.000
> | MDCRD: mdcrd.000
> |MDINFO: mdinfo.000
> | MTMD: mtmd
> |INPDIP: inpdip
> |RSTDIP: rstdip
> |INPTRA: inptraj
>
> | REMLOG: rem.log
> | REMTYPE: rem.type
> | REMSTRIP:
> | SAVEENE: saveene
> |CLUSTERINF: cluster.info
> | RESERVOIR: reserv/frame
> | REMDDIM:
>
>
> Here is the input file:
>
> minimization
> &cntrl
> imin=1,
> ncyc=1000,
> ntmin=2,
> maxcyc=5000,
> ntpr=50,
> cut=10.0,
> iwrap=1,
> icfe=1,
> clambda = 0.02,
> ifsc=1,
> scmask=':Nd',
> /
>
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
>
> --------------------------------------------------------------------------------
>
> | Flags: MPI
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> | peek_ewald_inpcrd: Box info found
> |Largest sphere to fit in unit cell has radius = 20.946
> | New format PARM file being parsed.
> | Version = 1.000 Date = 07/30/24 Time = 12:41:18
> NATOM = 4813 NTYPES = 12 NBONH = 2700 MBONA = 1959
> NTHETH = 5850 MTHETA = 2259 NPHIH = 8250 MPHIA = 2250
> NHPARM = 0 NPARM = 0 NNB = 22222 NRES = 304
> NBONA = 1959 NTHETA = 2259 NPHIA = 2250 NUMBND = 12
> NUMANG = 19 NPTRA = 11 NATYP = 13 NPHB = 0
> IFBOX = 1 NMXRS = 25 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
> | Memory Use Allocated
> | Real 1175018
> | Hollerith 14745
> | Integer 683637
> | Max Pairs 2772288
> | nblistReal 57756
> | nblist Int 286045
> | Total 24305 kbytes
>
> | 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
>
> BOX TYPE: RECTILINEAR
>
>
> --------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
>
> --------------------------------------------------------------------------------
>
> default_name
>
> General flags:
> imin = 1, nmropt = 0
>
> Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
>
> Nature and format of output:
> ntxo = 2, ntpr = 50, ntrx = 1, ntwr =
> 1
> iwrap = 1, ntwx = 0, ntwv = 0, ntwe =
> 0
> ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
> 0
>
> Potential function:
> ntf = 1, ntb = 1, igb = 0, nsnb =
> 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
> Energy minimization:
> maxcyc = 5000, ncyc = 1000, ntmin = 2
> dx0 = 0.01000, drms = 0.00010
>
> Free energy options:
> icfe = 1, ifsc = 1, klambda = 1
> clambda = 0.0200, scalpha = 0.5000, scbeta = 12.0000
> sceeorder = 2 dvdl_norest = 0
> dynlmb = 0.0000 logdvdl = 0
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme =
> 1
> vdwmeth = 1, eedmeth = 1, netfrc = 0
> Box X = 42.294 Box Y = 41.892 Box Z = 44.502
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 48 NFFT2 = 45 NFFT3 = 45
> Cutoff= 10.000 Tol =0.100E-04
> Ewald Coefficient = 0.27511
> Interpolation order = 4
>
> | MPI Timing options:
> | profile_mpi = 0
>
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
>
> default_name
> begin time read from input coords = 0.000 ps
>
> Number of triangulated 3-point waters found: 0
> | Atom division among processors:
> | 0 4813
>
> Softcore Mask :Nd; matches 1 atoms
> this run corresponds to V0, its softcore atoms interact fully for
> lambda=0
> this process: 4813 atoms, partner process: 4813 atoms
> Checking for mismatched coordinates.
> WARNING: Local coordinate 1 differs from partner coordinate 1
> !
> SANDER BOMB in subroutine sc_check_and_adjust
> Atom coordinate disagreement
> Check input files.
>
>
>
> On Aug 8, 2024, at 11:25 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> It looks like you turned on positional restraints (ntr=1) but may not have
> defined which atoms and what force constant.
>
> On Thu, Aug 8, 2024, 11:48 AM Weerawarna Kurukulasooriy, Sandaruwani
> Tharaka [CHEM] via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>>
> wrote:
> Dear Amber Community,
>
> I was trying to do the free energy calculation of the system I’m studying
> using the Thermodynamic Integration Technique. I changed the code given in
> the Tutorial a little bit according to my system. But the calculation stops
> after running for some time. I have attached the output that I am getting.
> It would be great if you could help. If any more information is needed I
> will gladly provide it
>
> File Assignments:
> | MDIN: mdin_min_v0_l0.02
> | MDOUT: Nd_IL3_min_v0_l0.02.out
> |INPCRD: Nd_IL3_0.rst
> | PARM: Nd_IL3.prmtop
> |RESTRT: Nd_IL3_min_v0_l0.02.rst
> | REFC: Nd_IL3_0.rst
> | MDVEL: mdvel.000
> | MDFRC: mdfrc.000
> | MDEN: mden.000
> | MDCRD: mdcrd.000
> |MDINFO: mdinfo.000
> | MTMD: mtmd
> |INPDIP: inpdip
> |RSTDIP: rstdip
> |INPTRA: inptraj
>
> | REMLOG: rem.log
> | REMTYPE: rem.type
> | REMSTRIP:
> | SAVEENE: saveene
> |CLUSTERINF: cluster.info<http://cluster.info/>
> | RESERVOIR: reserv/frame
> | REMDDIM:
>
>
> Here is the input file:
>
> minimization
> &cntrl
> imin=1,
> ncyc=1000,
> ntmin=2,
> maxcyc=5000,
> ntpr=50,
> cut=10.0,
> iwrap=1,
> ntr=1,
> icfe=1,
> clambda = 0.02,
> ifsc=1,
> scmask=':Nd',
> /
>
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
>
> --------------------------------------------------------------------------------
>
> | Flags: MPI
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> | peek_ewald_inpcrd: Box info found
> |Largest sphere to fit in unit cell has radius = 20.946
> | New format PARM file being parsed.
> | Version = 1.000 Date = 07/30/24 Time = 12:41:18
> NATOM = 4813 NTYPES = 12 NBONH = 2700 MBONA = 1959
> NTHETH = 5850 MTHETA = 2259 NPHIH = 8250 MPHIA = 2250
> NHPARM = 0 NPARM = 0 NNB = 22222 NRES = 304
> NBONA = 1959 NTHETA = 2259 NPHIA = 2250 NUMBND = 12
> NUMANG = 19 NPTRA = 11 NATYP = 13 NPHB = 0
> IFBOX = 1 NMXRS = 25 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
> | Memory Use Allocated
> | Real 1244270
> | Hollerith 14745
> | Integer 683637
> | Max Pairs 462048
> | nblistReal 57756
> | nblist Int 243000
> | Total 15654 kbytes
>
> | 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
>
> BOX TYPE: RECTILINEAR
>
>
> --------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
>
> --------------------------------------------------------------------------------
>
> default_name
>
> General flags:
> imin = 1, nmropt = 0
>
> Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
>
> Nature and format of output:
> ntxo = 2, ntpr = 50, ntrx = 1, ntwr =
> 1
> iwrap = 1, ntwx = 0, ntwv = 0, ntwe = 0
> ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
> 0
>
> Potential function:
> ntf = 1, ntb = 1, igb = 0, nsnb =
> 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 1
> restraint_wt = 0.00000
>
> Energy minimization:
> maxcyc = 5000, ncyc = 1000, ntmin = 2
> dx0 = 0.01000, drms = 0.00010
>
> Free energy options:
> icfe = 1, ifsc = 1, klambda = 1
> clambda = 0.0200, scalpha = 0.5000, scbeta = 12.0000
> sceeorder = 2 dvdl_norest = 0
> dynlmb = 0.0000 logdvdl = 0
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme =
> 1
> vdwmeth = 1, eedmeth = 1, netfrc = 0
> Box X = 42.294 Box Y = 41.892 Box Z = 44.502
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 48 NFFT2 = 45 NFFT3 = 45
> Cutoff= 10.000 Tol =0.100E-04
> Ewald Coefficient = 0.27511
> Interpolation order = 4
>
> | MPI Timing options:
> | profile_mpi = 0
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
>
>
> 5. REFERENCE ATOM COORDINATES
>
> defa
>
>
> Kind Regards,
>
> Sandaruwani Weerawarna
> Graduate Student
> Dr. Theresa Windus Lab
> Department of Chemistry
> Iowa State University
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 06/OG07
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 13 2024 - 23:30:02 PDT
