I don't understand what you're trying to do...
Is there a reason you deleted every residue except for those 3? By default,
leap turns any residue that's on one end of the TER card into a terminal
residue (the first is the N-terminus, the second is the C-terminus). Thus,
some atoms will have an OXT added to the residue to make it a carboxylate as
others will have an NH3+. If you choose not to terminate them (with a TER
card), then it will bond them according to their connect0 and connect1
atoms.
If you want to cap each, look into the caps ACE, NME, and NHE. However, I'm
really not sure what you're expecting to learn, since these amino acids
won't behave as they would in the entire protein, they'll just be floating
around like free amino acids...
Good luck!
Jason
On Tue, Jun 1, 2010 at 3:05 AM, Jio M <jiomm.yahoo.com> wrote:
> SORRY FOR PREVIOUS MAIL... I HAVE ATTACHED A TEXT FILE
>
>
>
> Dear Amber Users,
>
>
>
> Can anybody please suggest that whether I can do eq dynamics for
> discontinuous residues on pdb file like in attached file my.pdb
>
>
>
> here two problems are there:
>
>
>
> 1) If I dont insert TER between discontinued residue AMBER makes a bond
> between far residues like 495 and 70
>
>
>
> 2) If I insert TER between discontinued residues then AMBER considers
>
> and adds missing atom OXT. OXT is not desired as CO is free end.
>
> here no bond is formed as expected between far residues
>
>
>
> 3) Also if I remove added OXT atoms then the discontinous residues, as
>
> they are not bonded, will fly away during dynamics and it is not good
>
> to put positional restraints.
>
> So please suggest is it possible to dynamics in this case or I should
> consider the full sequence....
>
>
>
> thanks and regards,
>
> JIomm
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Jun 01 2010 - 07:30:10 PDT
