On Fri, Jan 15, 2010 at 6:27 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > ATOM 1 1HO ROH 1 2.144 0.950 -0.364 1.00 0.00
> > ATOM 2 O1 ROH 1 1.184 0.950 -0.364 1.00 0.00
> > ATOM 3 C1 0fA 2 1.154 -0.437 -0.084 1.00 0.00
> > ATOM 4 H1 0fA 2 2.168 -0.866 -0.126 1.00 0.00
> > ATOM 5 O5 0fA 2 0.313 -1.155 -0.937 1.00 0.00
>
> Do you have to treat the hydroxyl group as a separate residue? Maybe that
> is a glycam convention, but why not call the whole sugar 0fA? This
> shouldn't affect your results, though.
>
If I am calling whole sugar as 0fA but the residue number are same as
such 1 hydroxyl group and 2 for rest sugar then in that case xleap crushes
just after the loadpdb command in Xleap........error is fallowing..
> FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 142
> !FATAL: Message: Atom named C1 from 0fA did not match !
> !
> !ABORTING.
> [sushil.skirit storage]$
>
When I am calling whole sugar as 0fA but the residue number 1 for
hydroxyl group and rest sugar too then in that case xleap it doesnt find the
parameters for those atom types in GLYCAM forcefield. It loads the ligands
but and produces fallowing error. see the output of check command.
> check ligand
Checking 'ligand'....
ERROR: The unperturbed charge of the unit: 0.194000 is not integral.
WARNING: The unperturbed charge of the unit: 0.194000 is not zero.
FATAL: Atom .R<0fA 1>.A<CH3 22> does not have a type.
FATAL: Atom .R<0fA 1>.A<O 23> does not have a type.
Warning: Close contact of 2.003069 angstroms between .R<0fA 1>.A<C1 1> and
.R<0fA 1>.A<O 23>
Warning: Close contact of 1.864716 angstroms between .R<0fA 1>.A<CH3 22> and
.R<0fA 1>.A<O 23>
Checking parameters for unit 'l1'.
Checking for bond parameters.
Checking for angle parameters.
check: Errors: 3 Warnings: 3
> Is there any way to treat whole sugar as 1 molecule ?? What about the way
i used and discussed earlier....means with the same naming convention and
transformation of --H in to --CH3 ? Do u think this oxygen naming convention
will cause problem ?
Thanking You
Sushil
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Received on Fri Jan 15 2010 - 10:30:04 PST
