VMD-L Mailing List

From: Sujata Roy (sujataroy1_at_gmail.com)
Date: Sun Dec 07 2014 - 22:26:43 CST

Thank you very much
it worked
sujata

On Fri, Dec 5, 2014 at 11:33 AM, Ashar Malik <asharjm_at_gmail.com> wrote:

> Hi Sujata,
>
> From the charmm topology;
>
> Hydrogen on Beta carbon has charge of 0.09
> Oxygen on Asp - side chain is -0.76.
>
> I haven't used measure energy but i think that if you don't provide the
> charge information (q1 & q2) - they would be obtained from the PSF file
> (atom type). Which in the above case - would make sense if they are
> repulsive (not sure why though) however when you specify q1 and q2 you are
> giving them charges - which are opposite (and unrealistic - could you
> explain why you chose those charges) so naturally there would be a
> favourable interaction between them. I haven't used measure for the
> calculations of energies - but I would still recommend using "namdenergy"--047d7b4729126cd67d0509acd535--