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 in GLYCAM forcefield fir those atom types and produces fallowing
error
> 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
>
So
> > (ROH.O1) to methyl-fucose ":OME.O". So should i also include this atome
> > during the transformation and I shold go for transformation --OH to
> --OCH3
>
> The transformation -OH to -OCH3 should in the limit of sufficient sampling
> give the same free energy change as -H to -CH3 with O as common atom in
> both states. Depending on the different convergence and sampling of both
> cases, you will get slightly different results, though. I personally would
> not include the O in both scmasks, but either approach would be valid.
> Doing both is also a nice way to check for convergence of your results.
>
> Kind Regards,
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Fri Jan 15 2010 - 10:30:02 PST
