Actually I am working on the structure prediction of the polypeptide. I kept the side chains of the peptide as charged ones in explicit water. I carried out the intramolecular energy of peptide with neutral terminals (NH2 and COOH). Now I want to have the same terminals for the calculation of intermolecular interaction energy. From CHARMM, I had a force field with CNEU and NNEU (NH2 & COOH), but I want the explicit energy term for the hydrogen bonding pairs which is favoured by AMBERff. So is it possible to have such neutral terminals in amberff?
Thanks for any comments/suggestions.
Ramya.L.
On Tue, 16 Mar 2010 16:08:50 +0530 wrote
>we need more information about "neutral terminals". do you mean a blocking
group so that both are neutral, corresponding to an experiment with the
termini acetylated and amidated? these are included as ACE and NH2. if you
mean you want to simulation an extreme pH and have 1 of the two termini
neutral, tell us that. it's not physical to have the N- and C-termini both
neutral in water without blocking groups.
On Tue, Mar 16, 2010 at 3:56 AM, Ramya Narasimhan <
ramyashree_81.rediffmail.com> wrote:
>
>
> I want to use the amber99sb force field in NAMD program to calculate the
> solvation interaction energy. I tried with top_amber_cornell.inp &
> par_amber_cornell.inp. But I want to have neutral terminals as in CHARMm. Is
> it possible to do so? If yes, can I get the details regarding this?
>
>
>
> Thanks for any comments/suggestions
>
>
>
> Ramya
>
> Ramya. L.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 17 2010 - 00:30:02 PDT
