I think you misunderstand how this is supposed to work. You have up to three regions to define.
First, the common atoms which are completely identical in terms of _parameters_ and coordinates. Since you have chosen to use leap to create the prmtop file and obviously have two full copies of your protein system, you may want to delete redundant force field parameters, almost all of them _except_ where the system differs in parameters and/or number of atoms. You don't have to do that but you can save potentially a lot of computation time doing this in your case. You define these in the first two mask of tiMerge and they must match in size.
Second, you have the TI regions which in itself can be comprised of two sub regions. You will have to define every vanishing/appearing atom as a softcore atom. That's the minimum requirement but you can define more, up to all atoms in the TI region. The latter may be interesting if one wants to play around with "full" dual topology. Every atom that is not in the softcore subregion will have common coordinates _but_ differ in at least in one (typically the charge) force field parameter. There needs to be a one-to-one correspondence of this subregion and you must make this sure by ordering the atoms accordingly in prmtop. (Technically you can also include some/all common atoms from the first region but there are more interesting ways computing zeros...). 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.
The manual describing tiMerge tries to explain this ("nonsoftcore" as you use it is a misnomer). I think the part about the free energy implementation in the manual is a bit confusing in this.
Cheers,
Hannes.
________________________________________
From: fjliu [fjliu.itcs.ecnu.edu.cn]
Sent: 17 December 2014 07:51
To: AMBER Mailing List
Subject: Re: [AMBER] TiMergeError
I think that the number of nonsoftcore atoms must be the same refers to
" '1-520,1037-20160'(timask1) minus
'116,243,370,497,513-520,20157-20160' (scmask1)" have to equal to "
'521-1036,20161-39284'(timask2) minus
'636,763,890,1017,1033-1036,39281-39284'(scmask2) ". And in my case, the
timask1 is not equal to timask2 is because when the charged ASP mutated
to the uncharged ALA, the charge of the protein is increased, so I have
to remove the Na+ away in the mutation system to verify the charge of
the mutated system is zero, then I can derive the prmtop file.
Maybe I should limit the size of this system by taking just one chain
into consideration. Thanks!
On 17/12/14 15:20, hannes.loeffler.stfc.ac.uk wrote:
> The requirement for the common atoms is to have all the same coordinates. With the tolerance you can relax the check for this. But if you have created the inpcrd file from the same source then this should not be necessary.
>
> Your first two masks are not the same size. The water molecules are the same number but the protein part has a difference of 4 residues.
>
> Your common mask and your TI region mask overlap but they must be mutually exclusive. Also, you may want to limit the size of the TI region. Yours looks really large.
>
> ________________________________________
> From: fjliu [fjliu.itcs.ecnu.edu.cn]
> Sent: 17 December 2014 06:18
> To: amber.ambermd.org >> AMBER Mailing List
> Subject: [AMBER] TiMergeError
>
> Hello everyone,
> I have used the parmed.py module to prepare the parameter files for TI simulation(Mutation of a protein residue). There are something wrong:
>
> "TiMergeError: The number of nonsoftcore atoms in mol1mask and mol2mask must be the same. Check the masks. If these look correct try using a larger tolerance."
>
> I have checked the masks, the number of nonsoftcore atoms are identical. So I have to change the tolerance much larger, but I don't know where to change it.
> This is my input file:
>
> 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
> outparm complex_ti_merged_slv.top complex_ti_merged_slv.crd
> quit
>
> This is the step of VDW transformation. The complex have four chains, each of the chain has one residue mutated. "1037-20160 " and "39281-39284" represent the water box and include four crystal waters. There is no problem if I don't merge the water molecules. "513-520" and "1033-1036" represent the sodium for the change of charge once the ASP mutated to ALA. I don't know is that OK to remove the sodium when the ASP mutated to ALA during the TI simulation. Can you give me some advice about the free energy calculation with TI about the charged residue mutated to uncharged residue and do I need to duplicate the water box ? If there is a water molecule entranced once the residue mutated,how to consider this water molecule during the calculation? Is that right I replace the ASP to ALA-HOH? Look forward your advice and thanks!
>
> Best regards,
> Fengjiao Liu
>
>
>
>
>
>
>
>
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Received on Wed Dec 17 2014 - 00:30:02 PST
