Re: [gmx-users] pH and protein

On 7/12/12 1:42 AM, tarak karmakar wrote: Dear All, I am simulating a protein in gromacs with amber force field. The protein shows maximum biological activity at pH 5.0 and at pH 7.4 it shows no activity. So whichever biological process I am going to model should be at the biologically active

[gmx-users] pH and protein

Dear All, I am simulating a protein in gromacs with amber force field. The protein shows maximum biological activity at pH 5.0 and at pH 7.4 it shows no activity. So whichever biological process I am going to model should be at the biologically active pH . So can anyone suggest me 1) how to get

Re: [gmx-users] pH

On 9/05/2010 11:19 PM, pawan raghav wrote: Dear I have defined pH = 7.0 in mdp file according to tutorial but it shows an error. what is the criteria to set the different pH in .mdp file. There is surely no GROMACS tutorial that says this, because GROMACS lacks such a feature, for

[gmx-users] pH

Dear I have defined pH = 7.0 in mdp file according to tutorial but it shows an error. what is the criteria to set the different pH in .mdp file. -- Pawan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive a

Re: [gmx-users] PH 5.0 ?

Chih-Ying Lin wrote: HI How to assign charge for the residue of protein at PH 5.0 ? I have Ka values of each residue of protein then i can calculate the overall charge for each residue at PH 5.0 solution. However, how to calculate the partial charges of atoms within the residue of protei

[gmx-users] PH 5.0 ?

HI How to assign charge for the residue of protein at PH 5.0 ? I have Ka values of each residue of protein then i can calculate the overall charge for each residue at PH 5.0 solution. However, how to calculate the partial charges of atoms within the residue of protein at PH 5.0? Thank you Lin --

Re: [gmx-users] pH studies

On 11-10-2009 16:48, Justin A. Lemkul wrote: parthi...@ncbs.res.in wrote: Hi can any one could help me in, How to include the pH for doing MD studies. My interest is to include the pH at the initial time duration and to change the pH from 4 to 7 during the course of simulation. is there a

Re: [gmx-users] pH studies

parthi...@ncbs.res.in wrote: Hi can any one could help me in, How to include the pH for doing MD studies. My interest is to include the pH at the initial time duration and to change the pH from 4 to 7 during the course of simulation. is there any possibility in performing such work in gromacs

[gmx-users] pH studies

Hi can any one could help me in, How to include the pH for doing MD studies. My interest is to include the pH at the initial time duration and to change the pH from 4 to 7 during the course of simulation. is there any possibility in performing such work in gromacs. Thanks in advance Parthiban _

Re: [gmx-users] pH

Dmitriy Golubovsky wrote: Dear Guru! have you got any idea, on what how to calculate pH. for the system? i'm solving a promblem of coil-globule transition for polymer. do the topology for my structure(opls ff), do MD in water (spc). get the statiscts. everything is ok. the summary charge is eq

Re: [gmx-users] pH

> > 20 maj 2007 kl. 20.59 skrev David van der Spoel: > >> Dmitriy Golubovsky wrote: >>> Dear Guru! >>> have you got any idea, on what how to calculate pH. for the system? >>> i'm solving a promblem of coil-globule transition for polymer. >>> do the topology for my structure(opls ff), do MD in water

Re: [gmx-users] pH

20 maj 2007 kl. 20.59 skrev David van der Spoel: Dmitriy Golubovsky wrote: Dear Guru! have you got any idea, on what how to calculate pH. for the system? i'm solving a promblem of coil-globule transition for polymer. do the topology for my structure(opls ff), do MD in water (spc). get the st

Re: [gmx-users] pH

Dmitriy Golubovsky wrote: Dear Guru! have you got any idea, on what how to calculate pH. for the system? i'm solving a promblem of coil-globule transition for polymer. do the topology for my structure(opls ff), do MD in water (spc). get the statiscts. everything is ok. the summary charge is eq

[gmx-users] pH

Dear Guru! have you got any idea, on what how to calculate pH. for the system? i'm solving a promblem of coil-globule transition for polymer. do the topology for my structure(opls ff), do MD in water (spc). get the statiscts. everything is ok. the summary charge is equal to zero. no dissociation.

Re: [gmx-users] pH

Dhananjay wrote: Hello all, Will it be possible to calculate pH of the system just before and after adding hydrogens ? no, since you have no free H3O+ or OH- ions it is ill defined (log 0) If yes then how to calculate it ? Thanking you in advance. -- Dhananjay --

[gmx-users] pH

Hello all,Will it be possible to calculate pH of the system just before and after adding hydrogens  ?If yes then how to calculate it ?Thanking you in advance.-- Dhananjay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/