Your whole exercise is to reduce the prmtop to the absolute necessary!
So no need to have two descriptions of water as you are planning to
eliminate one copy anyway. You could only load that chain twice where
you are planning to do the perturbation, and possibly fiddle with
smaller subsets. You may have trouble to convince leap to accept small
fragments though. So it might be easier to use parmed to eliminate a
single chain.
I still do not understand why you believe that :1-520 and :521-1036
would be the two identical copies. The latter mask clearly has 4
residues less! You still have residues in scmask1 and scmask2 which
you also have in the first two masks (the last two ranges in the
third and fourth mask)... You are working with botched masks here, so
even if you manage to create a prmtop it will very likely be just as
botched.
I strongly suggest that you reread my previous answers and also the
manual.
Cheers,
Hannes.
On Wed, 17 Dec 2014 19:09:53 +0800
fjliu <fjliu.itcs.ecnu.edu.cn> wrote:
> Yeah, so I don't know what's wrong . It is write when I use the
> following script( which did not consider the water box):
>
> loadRestrt complex_ti_slv.crd
> setOverwrite True
> #tiMerge :1-520,1037-20160 :521-1036,20161-39284
> :116,243,370,497,513-520,20157-20160 :636,763,890,1017,1033-1036,39281-39284
> tiMerge :1-520 :521-1036 :116,243,370,497,513-520
> :636,763,890,1017,1033-1036
> outparm complex_ti_merged_slv.top complex_ti_merged_slv.crd
> quit
>
> Can I just use one water box for both the wild type complex and
> mutated system? Then I did not need to merge the two water box.
> On 17/12/14 17:24, Hannes Loeffler wrote:
> > On Wed, 17 Dec 2014 08:27:25 +0000
> > <hannes.loeffler.stfc.ac.uk> wrote:
> >
> >> You define those two subregions in the other two masks. Naturally
> >> they can be of different size. How you subpartition the TI region
> >> is a matter of the input file to pmemd not one of parmed.
> > Sorry, this is probably misleading. What the manual (section
> > 13.2.2.50, p. 243 in the current Amber14 manual) describes as
> > scmask1 and scmask2 should each be filled with what will be timask1
> > and timask2 in the input file (except in more complicated situation
> > where more masks may be needed as described in this section.)
> >
> > I feel that the manual needs some clarification regarding the terms
> > "common atoms" and "unique atoms". It looks to me that the tiMerge
> > entry and the section "Free energies" use two different definitions.
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Received on Wed Dec 17 2014 - 04:00:02 PST
