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.
>
> Cheers,
> Hannes.
>
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Received on Wed Dec 17 2014 - 03:30:02 PST
