On Fri, Nov 11, 2011, Crystal.CHIA-YU Ku wrote:
>
> Running: /home/crystal/amber11/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> Info: Bond types are assigned for valence state 1 with penalty of 1
> Running: /home/crystal/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
> Total number of electrons: 178; net charge: 1
> Running: /home/crystal/amber11/bin/sqm -O -i sqm.in -o sqm.out
> Error: cannot run "/home/crystal/amber11/bin/sqm -O -i sqm.in -o
> sqm.out" of bcc() in charge.c properly, exit
You need to look at the sqm.out file, which may (or may not) provide
some evidence about what went wrong.
>
> I checked the structure of the ligand, and realized the two oxygen of
> phosphate group had no hydrogen. Besides, one oxygen should be double
> bond. I do not know if no hydrogen on oxygen of phosphate caused the
> problem of running antechamber, so I trid Chimera to add H. But
> Chimera does not add H to these two oxygen. Do you know how I can add
> H to these two oxygen atom?
Well, if Chimera doesn't want to add an H atom, maybe it is not needed(?)
The fact that the bondtype command (above) did not complain is also a good,
but by no means definitive, sign.
Antechamber requires as input a good three-dimensional structure, with all
hydrogens present and the correct total charge. Without knowing anything
about your ligand, it's hard to say how to get from where you are to what you
need.
>
> I also followed the method provide by the link. Since my ff99SB uses
> ions94.lib, so I change ions94.cmd. But after changing ions94.cmd and
> typing "tleap -f ions94.cmd", xleap still fails to generate prmtop and
> inpcrd.
Does the error in LEaP point to the Mg2+ ion? You certainly can't get a good
prmtop until you solve the ligand problem discussed above. Try hard to parse
the error messages and warnings that LEaP gives you. I know they may be hard
to understand sometimes, but usually a careful reading pays dividends.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 11 2011 - 20:00:03 PST
