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 Fri Jun 02 2017 - 00:30:02 PDT
