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 - 09:30:02 PDT
