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 - 00:00:02 PST
