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 Wed Jun 28 2017 - 13:00:05 PDT
