Thank you. So what type you will choose? There seems to be no type in
AMBER for H+ ion in water. Aslo, I tried to add a H+ ion by add 3 lines
in pdb:
TER
ATOM 1232 H+ H+ 77 45.303 29.749 7.497 1.00 0.00
TER
But after I load this pdb and check the charge, it's still 0. While a
line
ATOM 1232 Li+ Li+ 77 45.303 29.749 7.497 1.00 0.00
can change the total charge to +1.
What code you will use to add H+ in leap? Or how you can edit the pdb
file to add a H+? Thank you so much.
----- Original Message Follows -----
> > I tried to add H+ to a pdb file using the code below, it seems fine,
> > but when I tried to save to pdb file, it failed as "Segmentation
> > fault". Any suggestions?
>
> There is clearly a bug.. another issue is:
>
> > > hp = createatom HP HW 1.000
>
> The vdw for HW is 0, so I would choose another type.
>
> Bill Ross
> ----------------------------------------------------------------------
> - The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Feb 17 2004 - 20:53:00 PST
