Hi,
Note that TI in sander requires the multisander functionality
which is only available in sander.MPI.
If plain sander reads an mdin with ifsc = 0 then an error will be
produced. For testing interactively it may be useful to run
sander.MPI with 1 processor.
scott
On Wed, Jun 28, 2017 at 12:58:33PM -0700, Bill Ross wrote:
> It is failing and you aren't getting an error message. Maybe you will
> see something if you run interactively.
>
> In the absence of more info, I would try with a simple min.in - if that
> fails too, then there is likely a problem with your model.
>
> I think restraints in min are more trouble than they are worth, unless
> you are consciously sculpting something.
>
> Bill
>
>
> On 6/28/17 12:53 PM, Sumudu Leelananda wrote:
> > Nope.
> >
> > This is all I get:
> >
> >
> > -------------------------------------------------------
> > Amber 14 SANDER 2014
> > -------------------------------------------------------
> >
> > | Run on 06/28/2017 at 10:47:03
> >
> > | Executable path: sander.MPI
> > | Working directory: /tmp/pbstmp.9464152
> > | Hostname: n0122.ten.osc.edu
> >
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN: step2_min0.in
> >
> > | MDOUT: step2_min0.out
> >
> > |INPCRD: protein_1CA6.inpcrd
> >
> > | PARM: protein_1CA6.prmtop
> >
> > |RESTRT: step2_min0.rst
> >
> > | REFC: protein_1CA6.inpcrd
> >
> > | MDVEL: mdvel
> >
> > | MDFRC: mdfrc
> >
> > | MDEN: mden
> >
> > | MDCRD: mdcrd
> >
> > |MDINFO: mdinfo
> >
> > | 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:
> >
> > System minimization:
> >
> > &cntrl
> >
> > imin=1, ntmin=2, nmropt=0, drms=0.1
> >
> > maxcyc=20000, ncyc=1500,
> >
> > ntx=1, irest=0,
> >
> > ntpr=500, ntwr=500, ntwx=500, iwrap=1,
> >
> > ntf=1, ntb=1, cut=10.0, nsnb=20,
> >
> > ntc=1,
> >
> > icfe = 1, ifsc = 0,
> >
> > clambda=0.5,
> >
> > ioutfm=1,
> >
> > nmropt=1/
> >
> > &wt type='DUMPFREQ', istep1=500, /
> >
> > &wt type='END', /
> >
> > DISANG=rest_step2.in
> >
> > DUMPAVE=rest.txt
> >
> > LISTIN=POUT
> >
> > LISTOUT=POUT /
> >
> > &end
> >
> >
> >
> >
> >
> >
> > --------------------------------------------------------------------------------
> > 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 = 33.907
> > | New format PARM file being parsed.
> > | Version = 1.000 Date = 04/14/17 Time = 10:45:04
> > NATOM = 25384 NTYPES = 16 NBONH = 24666 MBONA = 711
> > NTHETH = 1538 MTHETA = 960 NPHIH = 2969 MPHIA = 2332
> > NHPARM = 0 NPARM = 0 NNB = 39532 NRES = 8103
> > NBONA = 711 NTHETA = 960 NPHIA = 2332 NUMBND = 30
> > NUMANG = 61 NPTRA = 33 NATYP = 25 NPHB = 1
> > IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
> > NCOPY = 0
> >
> >
> > | Memory Use Allocated
> > | Real 2143344
> > | Hollerith 84257
> > | Integer 856534
> > | Max Pairs 1624576
> > | nblistReal 304608
> > | nblist Int 878284
> > | Total 32576 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
> >
> >
> > On Wed, Jun 28, 2017 at 3:51 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> Do you see energies being printed every 500 steps in the .out file?
> >>
> >> Bill
> >>
> >>
> >> On 6/28/17 12:47 PM, Sumudu Leelananda wrote:
> >>> This is Step2_min0.in
> >>>
> >>> I will try without mpi as well. Thank you.
> >>>
> >>> System minimization:
> >>> &cntrl
> >>> imin=1, ntmin=2, nmropt=0, drms=0.1
> >>> maxcyc=20000, ncyc=1500,
> >>> ntx=1, irest=0,
> >>> ntpr=500, ntwr=500, ntwx=500, iwrap=1,
> >>> ntf=1, ntb=1, cut=10.0, nsnb=20,
> >>> ntc=1,
> >>> icfe = 1, ifsc = 0,
> >>> clambda=0.5,
> >>> ioutfm=1,
> >>> nmropt=1/
> >>> &wt type='DUMPFREQ', istep1=500, /
> >>> &wt type='END', /
> >>> DISANG=rest_step2.in
> >>> DUMPAVE=rest.txt
> >>> LISTIN=POUT
> >>> LISTOUT=POUT /
> >>> &end
> >>>
> >>>
> >>>
> >>> On Wed, Jun 28, 2017 at 3:43 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >>>
> >>>> Please paste step2_min0.in here.
> >>>>
> >>>> Also, you might try without mpi.
> >>>>
> >>>> Bill
> >>>>
> >>>>
> >>>> On 6/28/17 12:29 PM, Sumudu Leelananda wrote:
> >>>>> I could not find any errors in that out file... Any hints?
> >>>>>
> >>>>> Thank you!
> >>>>>
> >>>>> On Wed, Jun 28, 2017 at 3:08 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >>>>>
> >>>>>> Look at step2_min0.out for clues as to why the rst wasn't generated.
> >>>>>>
> >>>>>> Bill
> >>>>>>
> >>>>>>
> >>>>>> On 6/28/17 12:05 PM, Sumudu Leelananda wrote:
> >>>>>>> Dear Dr. Loeffler
> >>>>>>>
> >>>>>>> Thank you for your suggestion. I tried it but it still gives the same
> >>>>>> error:
> >>>>>>> Error opening unit 30: File "step2_min0.rst" is missing or
> >> unreadable
> >>>>>>> I attached the inputs and also the output files for the charge step.
> >>>>>>>
> >>>>>>> mpiexec sander.MPI -O -i step2_min0.in -o step2_min0.out -c
> >>>>>>> protein_1CA6.inpcrd -p protein_1CA6.prmtop -r step2_min0.rst -ref
> >>>>>>> protein_1CA6.inpcrd
> >>>>>>>
> >>>>>>> mpiexec sander.MPI -O -i step2_min1.in -o step2_min1.out -c
> >>>>>>> protein_1CA6.inpcrd -p protein_1CA6.prmtop -r step2_min1.rst -ref
> >>>>>>> protein_1CA6.inpcrd
> >>>>>>>
> >>>>>>> mpiexec sander.MPI -O -i step2_heat0.in -o step2_heat0.out -c
> >>>>>>> step2_min0.rst -p protein_1CA6.prmtop -r step2_heat0.rst -x
> >>>>>> step2_heat0.nc
> >>>>>>> -ref step2_min0.rst
> >>>>>>>
> >>>>>>> mpiexec sander.MPI -O -i step2_heat1.in -o step2_heat1.out -c
> >>>>>>> step2_min1.rst -p protein_1CA6.prmtop -r step2_heat1.rst -x
> >>>>>> step2_heat1.nc
> >>>>>>> -ref step2_min1.rst
> >>>>>>>
> >>>>>>> mpiexec sander.MPI -O -i step2_md0.in -o step2_md0.out -c
> >>>>>> step2_heat0.rst
> >>>>>>> -p protein_1CA6.prmtop -r step2_md0.rst -x step2_md0.nc -ref
> >>>>>> step2_heat0.rst
> >>>>>>> mpiexec sander.MPI -O -i step2_md1.in -o step2_md1.out -c
> >>>>>> step2_heat1.rst
> >>>>>>> -p protein_1CA6.prmtop -r step2_md1.rst -x step2_md1.nc -ref
> >>>>>> step2_heat1.rst
> >>>>>>> Could you please give me suggestions or hints on this?
> >>>>>>>
> >>>>>>> Also, according to what you suggested it seems like we don't need a
> >>>>>>> restraint step when doing Sander? I can just only have the charge
> >>>> removal
> >>>>>>> step [2] and the van der Waals forces removal step [3]. Is that
> >> right?
> >>>>>>> Thank you!
> >>>>>>>
> >>>>>>> On Wed, Jun 28, 2017 at 12:18 PM, Sumudu Leelananda <
> >>>>>>> sumudu.leelananda.gmail.com> wrote:
> >>>>>>>
> >>>>>>>> Dear Dr. Loeffler
> >>>>>>>>
> >>>>>>>> Thank you for your suggestion. I tried it but it still gives the
> >> same
> >>>>>>>> error:
> >>>>>>>>
> >>>>>>>> Error opening unit 30: File "step2_min0.rst" is missing or
> >>>> unreadable
> >>>>>>>> I attached the inputs and also the output files for the charge step.
> >>>>>>>>
> >>>>>>>> Could you please give me suggestions on this?
> >>>>>>>>
> >>>>>>>> Also, according to what you suggested it seems like we don't need a
> >>>>>>>> restraint step when doing Sander? I can just only have the charge
> >>>>>> removal
> >>>>>>>> step [2] and the van der Waals forces removal step [3]. Is that
> >> right?
> >>>>>>>> Thank you!
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On Fri, Jun 2, 2017 at 3:19 AM, Hannes Loeffler <
> >>>>>>>> Hannes.Loeffler.stfc.ac.uk> wrote:
> >>>>>>>>
> >>>>>>>>> On Thu, 1 Jun 2017 15:22:53 -0400
> >>>>>>>>> Sumudu Leelananda <sumudu.leelananda.gmail.com> wrote:
> >>>>>>>>>
> >>>>>>>>>> Dear Hannes
> >>>>>>>>>>
> >>>>>>>>>> Thank you for your reply. I'm sorry, I only got a part of your
> >>>> reply
> >>>>>>>>>> and don't see the full reply on the archives yet. Yes. I'm using a
> >>>>>>>>>> similar multisite Calcium model but the number of dummy atoms is
> >>>>>>>>>> different than Sept Model you provided the link to.
> >>>>>>>>>>
> >>>>>>>>>> In PEMED I had 2 Ca ions in the restraint step (residue numbers 90
> >>>>>>>>>> and 91). What I do is restraint 90 at the end of the restraint
> >> step.
> >>>>>>>>>> Then in the charge step remove the charge from 91 and in the vdW
> >>>> step
> >>>>>>>>>> totally remove 91. PEMED calculations worked without any issues.
> >>>>>>>>>> Issues arise for Sander.
> >>>>>>>>> So step 2 would be
> >>>>>>>>> icfe = 1, ifsc = 0,
> >>>>>>>>> timask1 = ':90', timask2 = ':91',
> >>>>>>>>> crgmask = ':91'
> >>>>>>>>>
> >>>>>>>>> And step 3
> >>>>>>>>> icfe = 1, ifsc = 1, scalpha = 0.5,
> >>>>>>>>> timask1 = ':90', timask2 = '',
> >>>>>>>>> scmask1 = ':90', scmask2 = ''
> >>>>>>>>> crgmask = ':90'
> >>>>>>>>>
> >>>>>>>>> Step 3 obviously implies that you don't have a residue 91.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>> In Sander which I'm doing now, I didn't see the need to have two
> >>>>>>>>>> copies like that so I only have 90.
> >>>>>>>>> Sander needs two topology files and two input files, and it doesn't
> >>>>>> have
> >>>>>>>>> timask.
> >>>>>>>>>
> >>>>>>>>> So 2a:
> >>>>>>>>> icfe = 1, ifsc = 0,
> >>>>>>>>>
> >>>>>>>>> and 2b
> >>>>>>>>> icfe = 1, ifsc = 0,
> >>>>>>>>> crgmask = ':90'
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> 3a:
> >>>>>>>>> icfe = 1, ifsc = 1, scalpha = 0.5,
> >>>>>>>>> scmask = ':90'
> >>>>>>>>> crgmask = ':90'
> >>>>>>>>>
> >>>>>>>>> 3b:
> >>>>>>>>> icfe = 1, ifsc = 1, scalpha = 0.5,
> >>>>>>>>> scmask = ''
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Received on Thu Jun 29 2017 - 20:30:02 PDT
