Charge assignment is dependent on forcefield. If the forcefield results in integral charges for polar residues then that's what you get. (Most classical FFs do.)
I could be wrong but I don't think gromacs supports polarizable forcefields. On 2012-04-07 02:21:42AM -0700, Acoot Brett wrote: > Thanks Francesco. > > But at any pH value (different protonation state), the H cannot be regarded > as fully associated or dissociated. Thus can we further consider whether the > total charge calculated by pdb2gmx is really the net charge of the system or > not. I regard the net total charge, regardless of positive or negative, can > hardly be an integer. > > Furthermore, if we do not add couter ions to make the net charge "0" for the > whole system and we do the MD, what can occur? > > Cheers, > > Acoot > > > ________________________________ > From: Francesco Oteri <francesco.ot...@gmail.com> > To: gmx-users@gromacs.org > Sent: Saturday, 7 April 2012 7:14 PM > Subject: Re: [gmx-users] how pdb2gmx calculate the total charge of a protein > > > Dear Acoot, > the error, I guess, is you assumed the histidines are positive while > I think they are neutral. > Since the His protonation state is hard to identify at ph7, > Hystidines are usually neutral. > > Francesco > > > Il 07/04/2012 09:42, Acoot Brett ha scritto: > > > Dear All, > > > >I have a protein, the charged residue numbers in the protein is as following > >ARG 11 > >ASP 19 > >glu 25 > >his 8 > >lys 24 > > > >asp+glu= 44 > >arg+his+lys=43 > > > >However the total charge of the protein given by pdb2gmx is -9. > > > >Will you please introduce to me how pdb2gmx calculate the total charge of > >the protein? > > > >Cheers, > > > >Acoot > > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
