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 - 13:00:03 PDT
