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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> >>
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Received on Wed Jun 28 2017 - 12:30:05 PDT
