On Mon, Dec 17, 2012, Thomas Evangelidis wrote:
>
> I created a tip4pew.pdb file with the following contents:
>
> ATOM 1 O TP4 1 12.718 8.873 8.539 0.000
> ATOM 2 H1 TP4 1 12.637 7.958 8.269 0.524220
> ATOM 3 H2 TP4 1 12.304 9.370 7.833 0.524220
> ATOM 4 EPW TP4 1 12.654 8.820 8.414 -1.048440
> TER
>
> and used it with AddToBox to fill up with TIP4P-Ew waters a predefined box.
AddToBox creates an updated pdb file; it knows nothing about charges, and
would ignore the final column in the pdb file above.
> However, when I loaded it in VMD and checked the partial charges I found
> the following inconsistencies:
What is the "it" that you loaded into VMD?
>
> 0.0 0.5199998617172241 0.5199998617172241 -1.0399997234344482
The above charges are for the (original) Tip4p model.
> instead of 0.0 0.5242198705673218 0.5242198705673218 -1.0484397411346436,
The above charges are for TIP4P-Ew.
> How can I load in leap TIP4P-Ew waters in a .pdb file and write a correct
> .prmtop file?
Here is a possible answer (depending on exactly what you did): in the
solvents.lib file (which is loaded from many of Amber's leaprc file), "TP4"
is the name of the original Tip4p water model, and "T4E" is the name of
residues with the TIP4P-Ew model. So, if you loaded your pdb file (above)
into LEaP, the charges that are there are ignored, but the TP4 residue name
would trigger loading the original TIP4P charges. See if changing the residue
name to T4E helps.
....dac
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Received on Mon Dec 17 2012 - 06:00:07 PST
