[gmx-users] A common error Atom O11 in residue bDM 1 was

You are right Justin, The 1O1 atoms and (others 1O2, etc.) are changed to O11, O21, etc. (?). Why this problem happens ? Should I change the name of these atoms in the rtp and pdb files ? Is a trick is available to avoid this "bad" translation ? Stefane ABEL Stephane 175950 wrote: > Dear a

Re: [gmx-users] A common error Atom O11 in residue bDM 1 was

ABEL Stephane 175950 wrote: You are right Justin, The 1O1 atoms and (others 1O2, etc.) are changed to O11, O21, etc. (?). Why this problem happens ? Should I change the name of these atoms in the rtp and pdb files ? Is a trick is available to avoid this "bad" translation ? The only option i

[gmx-users] About COM pulling

Hi all,    I am using GMX4.5.1 to do COM pulling .    ; COM PULLING          ; Pull type: no, umbrella, constraint or constant_forcepull                     = umbrella; Pull geometry: distance, direction, cylinder or positionpull_geometry            = direction; Select components for the pull ve

Re: [gmx-users] About COM pulling

zhongjin wrote: Hi all, I am using GMX4.5.1 to do COM pulling . ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = umbrella ; Pull geometry: distance, direction, cylinder or position pull_geometry= direction ; Select c

[gmx-users] electrostatics with non-periodic system

Hi all, Could anybody please suggest "a good method" for electrostatics for non-periodic system simulation -> PBC=no ? Let's say it is pure water system. -- Dr. Vitaly V. Chaban Department of Chemistry University of Rochester Rochester, NY 14627-0216 United States of America -- gmx-users mailin

RE: [gmx-users] vanadium non-bonded parameters

See Manual, 5.3.3 Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9909 9304 - When the only tool you own is a hammer,

[gmx-users] How to make a lipid bilayer with specific dimensions?

Dear gmxusers, I am trying to make a lipid bilayer with specific dimensions using gromacs. So far, I have got up to: 1) Download a lipid POPC128a.pdb from Peter Tieleman's website 2) Use genconf -f popc128a.pdb -o popcx2.pdb -nbox 2 2 1 to multiply the lipid in the x and y ax

[gmx-users] Query regarding protonation and deprotonation of some residues

Hello All, I came through this research article, in which author has selectively deprotonated and protonated some of the residues to simulate the condition for electrostatic interaction with the substrate while carrying out molecular dynamics simulation. It will be appreciable, if you could help

Re: [gmx-users] Query regarding protonation and deprotonation of some residues

Hi, You need to define the protonation sate vie pdb2gmx. pdb2gmx -tyr -lys On 27/09/10 2:34 PM, sonali dhindwal wrote: Hello All, I came through this research article, in which author has selectively deprotonated and protonated some of the residues to simulate the condition for electrostat

[gmx-users] Reg: Adding multiple molecules

Hi all I have a diffculty in adding multiple molecules of hexane to my box. my box size is 4.72*2.36*2.36 (nm) according to my number density calculations the box should fit 124 molecules of hexane whereas it adds only 76 molecules to the box below is my command. i had evev tried with -try command

RE: [gmx-users] electrostatics with non-periodic system

Hi, For pure water (no ions, no external electric field), reaction field does fine even with a short cut-off, e.g. 0.9 nm (use reaction-field-zero if you need good energy conservation). In case you have long-range fields, use no-cutoff at all (all cut-off to 0 in the mdp file) when you system i

Re: [gmx-users] Query regarding protonation and deprotonation of some residues

Thanks Kass for the help. I want to specifically protonate one of the lysine near the active site and deprotonate Tyr and Ser. It will be kind if  you can please help me to know how to select that specific residue number. Regards -- Sonali Dhindwal --- On Mon, 27/9/10, Itamar Kass wrote: Fro