David is right. You just need to change the names/numbers of the
sugar residues/atoms in the pdb file containing the protein and sugar.
It is safest also to make sure there is a TER card after the sugar if
there are any other atoms following it in the file. (x|t)Leap will
probably recognize the waters as separate, but there's no harm in
adding the TER card, just in case you have accidentally done something
incorrect with the sugar renaming, and in case there is some other
molecule lurking below.
In VMD or Chimera, check especially that the bonds within the sugar
are correct and that there are no unwanted bonds between the sugar and
other molecules.
On Tue, May 26, 2015 at 7:35 AM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Tue, May 26, 2015, Chris wrote:
>>
>> As I say, I want prepare parameters for protein and a monosaccharide
>> (non-bounded) in a crystal PDB structure, not a sugar alone.
>
> This sounds like a distinction without a difference: if the sugar is not
> covalently bonded to the protein, then one prepares amber library files and
> pdb files in exactly the same way, whether or not a protein is present.
> Make sure there is a TER card in your pdb file between the protein parts and
> the sugar parts.
>
>> Question comes: Such handling is OK and reasonable???( Personally, I
>> think it is OK, I have checked the structure after this)
>
> What you have described sounds OK to me. Of course, check things yourself:
> e.g. run a minimization of the complex, visualize the resulting structure in
> some program like VMD or Chimera, and make sure it looks like what you think
> it should.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 26 2015 - 10:30:02 PDT
