[gmx-users] NEUTRALISED CHARGES

hello gromacs i am trying to minimise my protein-ligand complex in gromacs.but it shows that system has non zero charge can any body says how much *cl ion*, i have to add to neutralised it. i am terminal window text. thank u -- AKALABYA BISSOYI N.I.T.Rourkela system Description: Binary data

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir, Greetings from Pawan. Thanks for all your suggestions and help. The solvation is completed and the system is neutralized. The position restraint mdrun and final mdrun has worked out successfully without any warnings and errors this time. The structure after the final mdrun is not qu

[gmx-users] editconf 2 warning

Hi These 2 warning appeared after I did editconf for Drug-Protein Complex. WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type WARNING: vdwradii will be determined based on residue and atom names, this can d

RE: [gmx-users] editing .rtp files

Another to keep an eye out for, is make sure that you edited the correct .rtp file you tell pdb2gmx to use when running it. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 301

RE: [gmx-users] problem in topology file for protein+lipid bilayer system

May be have bit of a read of http://wiki.gromacs.org/index.php/Category:Force_Fields and the manual, so you can get a grip on what forcefields actually are and how you use them. I get the impression you are trying to do things here without actually understanding or even thinking about what you are

RE: [gmx-users] density around protein

Or g_sdf Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is

Re: [gmx-users] broken molecules in ouput of MDRUN

Gurpreet Singh wrote: Dear Users, I am simulating a binary mixture of cyclohexane-water using gromacs 4.0.4. Every thing works fine except that the output trajactory (.xtc file) contains broken molecules. Interestingly enough, as the last frame of simulation is also dumped as gro file, has

[gmx-users] broken molecules in ouput of MDRUN

Dear Users, I am simulating a binary mixture of cyclohexane-water using gromacs 4.0.4. Every thing works fine except that the output trajactory (.xtc file) contains broken molecules. Interestingly enough, as the last frame of simulation is also dumped as gro file, has all the molecules as

Re: [gmx-users] energy

jayant james wrote: Hi! I ran a simulation for 1ns and I find that the energy file has been written only till 627 ps. I am wondering how to extend my simulations as I need the energy file (simulated with 1bar pressure)!!! I wonder why this is happening on a consistent basis. I cannot think of

[gmx-users] energy

Hi! I ran a simulation for 1ns and I find that the energy file has been written only till 627 ps. I am wondering how to extend my simulations as I need the energy file (simulated with 1bar pressure)!!! I wonder why this is happening on a consistent basis. I cannot think of the energy file being la

Re: [gmx-users] editing .rtp files

Jacob Harvey wrote: Thanks for your help Justin. Looks like I am still having issues though. Now I get the error: "Fatal error: Residue 'IMD' not found in residue topology database" I am trying to create a topolgy file using pdb2gmx with the OPLS-AA force field and I have added the following

Re: [gmx-users] editing .rtp files

Thanks for your help Justin. Looks like I am still having issues though. Now I get the error: "Fatal error: Residue 'IMD' not found in residue topology database" I am trying to create a topolgy file using pdb2gmx with the OPLS-AA force field and I have added the following entry to the ffoplsaa.rt

Re: [gmx-users] density around protein

g_sorient returns the number of solvent molecules within a given distance range of a protein -- it may be what you are looking for. Matt 2009/4/5 Morteza Khabiri : > Dear gmxusers > > I want to calculate the density of solvent around protein. > I already tried the commands g_density and g_densmap

[gmx-users] density around protein

Dear gmxusers I want to calculate the density of solvent around protein. I already tried the commands g_density and g_densmap but the results are not the the things that I want. The g_density Compute partial densities across the box and g_densmap just give me one black and white photo which don't

[gmx-users] dgdl convergence in free energy calculation

Dear all, I am calculating the mutation free energies using TI method for a small globulin protein which contains about 40 residues. I meet convergence problems in the FE calculations: (1) when simulations start with different velocities for the some lambda points, the variance of dGdlamba is big

RE: [gmx-users] problem in pulling in gromacs 4.03

Hi, I think this is a bug in 4.0.3. Please switch to 4.0.4. Berk Date: Sat, 4 Apr 2009 22:00:44 +0530 From: polley.anir...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] problem in pulling in gromacs 4.03 Dear sir, I want to pull a small protein molecule (GPI) which is i