Re: [gmx-users] parameter for iron(HEME) and S-Cys

Zhanglin Ni wrote: Dear all, The pdb2gmx can find the special bonds such as the coordinate covalent bond between CYS-S and Iron of HEME, but the library for example ffG53a6bon.itp doesnot contains the parameters for bond angle such as S-Fe-NR(heme), bond or dihedral torsional angles. Any sug

Re: [gmx-users] (no subject)

chandrabhan seniya wrote: hello sir.. i have a problem in running pdb2gmx command fatal error is : atom c1 in residue na+ 369 not found in rtp entry with 1 atom while soting atoms Please use a descriptive email subject, and a full description of your problem. Copied and pasted inputs and out

[gmx-users] mdp file to calculate local pressure

Dear Sir, I am looking for local pressure where I am using gromacs-4.0.2_localpressure.tarpackage. I have download it from ftp://ftp.gromacs.org/pub/tmp The error which it gives during

Re: [gmx-users] mdp file to calculate local pressure

anirban polley wrote: Dear Sir, I am looking for local pressure where I am using gromacs-4.0.2_localpressure.tar package. I have download it from ftp://ftp.gromacs.org/pub/tmp

[gmx-users] problem in neutralising my system

Dear all I am facing a problem in neutralizing my system which has total nonzero charge :- -1.161999e+01 . so can any one suggest me how much positive charge i have to add my system.? I am asking this question becoz i alredy tried to neutrilise when I added +12 np th

Re: [gmx-users] problem in neutralising my system

nitu sharma wrote: Dear all I am facing a problem in neutralizing my system which has total nonzero charge :- -1.161999e+01 . so can any one suggest me how much positive charge i have to add my system.? I am asking this question becoz i alredy tried to neutrili

[gmx-users] Why NaCl and KCl solution?

HI 1. Would you please tell me the reason that "generally people use NaCl or KCl in the solution with protein"? 2. Why does PDB file of the protein NOT Carrying ions? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gro

Re: [gmx-users] Why NaCl and KCl solution?

Chih-Ying Lin wrote: HI 1. Would you please tell me the reason that "generally people use NaCl or KCl in the solution with protein"? You might want to read some basic biochemistry textbook. Without salt you die. 2. Why does PDB file of the protein NOT Carrying ions? Thank you Lin ___

Re: [gmx-users] Why NaCl and KCl solution?

Chih-Ying Lin wrote: HI 1. Would you please tell me the reason that "generally people use NaCl or KCl in the solution with protein"? 2. Why does PDB file of the protein NOT Carrying ions? PDB structures do not contain information about the properties of the solvent or precipitant used

[gmx-users] The default pH =7.0 ???

Hi Does the Gromacs set the default pH = 7.0 ? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't

[gmx-users] The default pH =7.0 ??? and the protonation state after pdb2gmx

Hi after the command pdb2gmx, the protein will be added appropriate H, So, does pdb2gmx add H (protonate) based on pH =7.0 ? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please searc

[gmx-users] Counter ions added

Hi I search some papers based on MD. Most of them did not tell what the counter ions they added. Why? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http:/

Re: [gmx-users] The default pH =7.0 ???

Chih-Ying Lin wrote: Hi Does the Gromacs set the default pH = 7.0 ? No. This also isn't a meaningful question for an explicit-solvent simulation. If you'd done the calculation I suggested yesterday (http://www.gromacs.org/pipermail/gmx-users/2009-May/042128.html) then you'd already appreci

Re: [gmx-users] The default pH =7.0 ??? and the protonation state after pdb2gmx

Chih-Ying Lin wrote: Hi after the command pdb2gmx, the protein will be added appropriate H, So, does pdb2gmx add H (protonate) based on pH =7.0 ? No. You should choose the protonation state based on your understanding of the conditions you wish to model, and instruct pdb2gmx accordingly. Rea

Re: [gmx-users] Counter ions added

Chih-Ying Lin wrote: Hi I search some papers based on MD. Most of them did not tell what the counter ions they added. Why? They may have been implicit solvent MD where none are added, or their simulation system may have been neutral, or they may have used a model physics where a net charge i

[gmx-users] question about force field parameter

Dear all I am a little confused with some force field parameter library. for example #define gd_26 0.000 2.93 3 ; -CH2-S- 0.7 dihedral is supposed to be i j k l 4 atoms , why, for example, the case above has only 2 atoms. thanks Johnny

Re: [gmx-users] question about force field parameter

Zhanglin Ni wrote: Dear all I am a little confused with some force field parameter library. for example Whether and how this makes sense depends on the context, which you need to tell us, since we are not going to go looking and guessing for you. :-) #define gd_26 0.000 2.93