Professor Case,
Thank you for your attention.
On 17 December 2012 15:33, David A Case <case.biomaps.rutgers.edu> wrote:
> 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?
>
My apologies for the confusion. I meant the .prmtop and .inpcrd files I
created with LEaP using the outpout of AddToBox.
> >
> > 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.
>
>
Yes, that worked for the charges and atom names. Is there any other
attribute I could check to make sure I am using the correct water model?
thanks,
Thomas
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Received on Mon Dec 17 2012 - 07:00:04 PST
