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 - 12:30:03 PDT
