Respected Case,
Thanks for your reply. I want to simulate my system at low pH. For this
purpose, i protonated acidic amino acids, which made protein highly
positive. I further proceeded as suggested in tutorials (eg using leap ->
solvated --> added Ions ---> saved top and crd ). This system (solvated and
with Cl ions) gives high positive energy. Is the simulation of above
charged system without ions, valid? Please, suggest me. I am seeking for
your reply.
Thanks in advance..
with best regards
Kshatresh
On Sat, May 7, 2011 at 6:44 PM, case <case.biomaps.rutgers.edu> wrote:
> On Sat, May 07, 2011, Kshatresh Dutta Dubey wrote:
> >
> > I am trying to simulate a positive charged dimeric protein. I solvated
> the
> > system using TIP3P box and added Cl- to neutralize the system. During
> > minimization, i got high positive value of EAMBER as well as other energy
> > contributions which causes errors during dynamics. However, when i am not
> > adding Cl- ions in system (system remains positive charge), energy of
> system
> > is negative and dynamics runs properly. Is simulation of charged system (
> > without adding Cl ions) valid?
>
> It is valid to run without ions, but you should try to find out why you got
> the problems you report.
>
> In your message (as with many on the list posted by others) you tell us
> what you *intended to do* (add ions and run minimization/dynamics), but
> not what you *actually did* (the commands you ran, and important features
> of the results). Without the latter information, no one will be able to
> help you. Be sure you are doing things similar to the procedures shown in
> the tutorials, such as the very first one.
>
> ...dac
>
>
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>
--
**************************************************************************************************************************
Kshatresh Dutta Dubey
Senior Research Fellow (SRF)
Biophysics Unit,
Department of Physics
DDU Gorakhpur University
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Received on Sat May 07 2011 - 07:30:02 PDT
