Mahendra,
Are you simply asking how the charge of the system is determined? That is
simply a function of the partial atomic charges assigned by the force
field. In the standard AMBER force field I believe these are meant to
correspond to the protonation state of the isolated residues at pH ~7. For
DNA all bases and sugars are therefore neutral and phosphate diesters are
monoanionic.
There may be good reason to change (some of) the protonation states in
large systems, but such a residue is probably non-standard (although in
principle it could be derived straightforwardly via RESP, see RED Server
for example).
Regards,
Brian
On Tue, Jan 22, 2013 at 5:41 PM, Mahendra B Thapa <thapamb.mail.uc.edu>wrote:
> Dear AMBER users,
>
> We add ions ( either Na or Cl) to make the
> system neutral; I am interested to know how we can determine the total
> amount of charge of the system( say, protein). For example, in the tutorial
> 1, section 2 , sub-section2.3.1, 18 sodium anions are added to counteract
> the -18 charge of the DNA chain. Similarly, in my system , I have added
> the different number of Na-ions using addions command. What is the theory
> behind it? If possible, please suggest also the relevant papers or other
> materials .
>
> Thanks,
> Mahendra Thapa
> Graduate Student(Physics)
> University of Cincinnati
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 23 2013 - 06:30:03 PST
