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 - 13:00:04 PDT
