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 - 12:30:04 PDT
