Hello Amberers,
lately I work on simulations with calcium ions and I noticed it is quite
complicated to use that ion in AMBER in comparison to other ions. There
is atom type C0 defined for calcium ions in amber params e.g.:
dat/leap/parm/parm99.dat:
C0 40.08 calcium
but the same atom type is used for carbon with hybridization sp2 e.g.:
dat/leap/cmd/leaprc.ff99SB:
addAtomTypes {
{ "C0" "C" "sp2" }
}
This is quite confusing and could cause quite a mess. Together it even
destroys calcium ion residue defined in GLYCAM_06:
$ tleap -f leaprc.ff99SB
> loadamberprep GLYCAM_06.prep
> desc CA2.1.1
...
Name: CA2
Type: C0
Charge: 2.0000
...
Element: C
...
Can you resolver this issue? For my own simulations I have copied ff99SB
and removed C0 from addAtomTypes command, but I am not sure if this is
generally good idea. It would be also nice to have Ca2+ ion defined in
libraries with other ions.
Regards,
Vlastimil
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 31 2012 - 05:30:05 PST
