AMBER Archive (2008)

Subject: Re: AMBER: Querry

From: Lachele Foley (Lists) (lf.list_at_gmail.com)
Date: Wed Aug 13 2008 - 10:03:49 CDT

The GLYCAM06 force field contains parameters for O-linking sugars to
threonine. Section 3.5.3 of the AmberTools manual contains
information regarding use of the parameters in this situation. Write
back if you have additional problems or if the instructions there do
not address your situation.

Also, the "bridging hydrogen" issue might indicate use of the wrong
residues or residue names. If you think this might be a problem, I
suggest looking over all of section 3.5 in the manual. It contains a
fairly detailed description of the procedures for naming and building
oligosaccharides. Again, write back if you continue to have
difficulty.

:-) Lachele

On Wed, Aug 13, 2008 at 10:48 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> Hi Dipti,
>
>
>
> Stop for a minute and read the error message more carefully. Leap is telling
> you that the hydrogen atom H1 of residue 20 will have it's maximum
> coordination exceeded if it is bonded to atom 11 of residue 11. This seems
> to be a perfectly clear and reasonable error message to me. I assume you
> don't want a bridging hydrogen atom here. Go back and check that the
> residues have the correct protonation states (you may need to build your own
> custom ones) and that the atom numbers you are giving to the bond command
> are also correct.
>
>
>
> Be aware that the next error you are likely to see will be missing
> parameters for this bond so if you haven't already you should take a look at
> the A1 tutorials on the AMBER site so you know how to create the frcmod file
> you will need. You should also check the literature to see what people
> typically do for the bond between the sugars and the protein.
>
>
>
> Good luck,
>
> Ross
>
>
>
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> dipti lele
> Sent: Wednesday, August 13, 2008 5:15 AM
> To: amber_at_scripps.edu
> Subject: AMBER: Querry
>
>
>
> Hello All,
>
> I am working with a glycopeptide. And during the simulation the bond
> between the threonine and sugar was seen to be broken. I realised that there
> was no bond present right from the beginning. I tried to use leap and
> command BOND to create a bond. But it gave me following error :
>>bond y.11.11 y.20.2
> Bond: Maximum coordination exceeded on .R<3VA 20>.A<H1 2>
> -- setting atoms pert=true overrides default limits
>
> What Should I do else to solve the problem.
>
> Thanking you !!
>
>
> --
> Deepti Lele,
> NII, New Delhi. 

-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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