[gmx-users] Re: topology file generation for a modeled structure

Hi all, I have modelled a structure and I want to minimize it using GROMACS but while generating the topology file using pdb2gmx command I am getting the following error :- Atom HN1 in residue LEU 1 not found in rtp entry with 9 atoms while sorting atoms. Maybe different protonation

Re: [gmx-users] Re: topology file generation for a modeled structure

Hello! Since you have modelled the structure, so the important thing is the position of the heavy atoms and not of the hydrogens, you can just do what GROMACS asks you to do: pdb2gmx . (all the things that you have to put) .. -ignh This flag will make pdb2gmx ignore the hydrogens and

Re: [gmx-users] Re: topology file generation for a modeled structure

Thanks for the help mdrun step is going on now .. but I wanna ask one thing that how can I visualize the minimized structure .. The structure which I used initially is the minimized structure or not ?? Bharat M.Sc. Bioinformatics (Final year) Centre for Bioinformatics Pondicherry University

[gmx-users] best interval for saving configurations ?

Hi all What is the best interval for saving configurations in full md step? (every what ps?) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post

[gmx-users] how to extract the LJ interaction parameters from the tpr file

Hi all, I want to calculate the non-bonded interactions (LJ+Coulomb) between two sub-groups when they are within the cutoff distance. The sub-groups are only parts of the whole energy groups used in my .mdp file. Given the partial charges of the atoms involved are easy to get from the

Re: [gmx-users] how to extract the LJ interaction parameters from the tpr file

On 08/02/10 21:03, Baofu Qiao wrote: Hi all, I want to calculate the non-bonded interactions (LJ+Coulomb) between two sub-groups when they are within the cutoff distance. The sub-groups are only parts of the whole energy groups used in my .mdp file. Given the partial charges of the atoms

Re: [gmx-users] mdrun append problem

Chandan Choudhury wrote: Hello gmxusers !! gmxcheck on #spc_25_eq.trr prints: (#spc_25_eq.trr is the renamed from #spc_25_eq.trr.1#. mdrun was stopped due to insufficient space) Checking file #spc_25_eq.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 2000.000 #

[gmx-users] Re: Minimized structure

Hi all, I had followed all the 7 steps of gromacs beginners tutorial and I have a doubt that during the minimization step .. which structure is minimized one ?? The one that i used for the minimization step ... Pls reply -- Bharat M.Sc. Bioinformatics (Final year) Centre for Bioinformatics

Re: [gmx-users] Re: Minimized structure

bharat gupta wrote: Hi all, I had followed all the 7 steps of gromacs beginners tutorial and I have a doubt that during the minimization step .. which structure is minimized one ?? The one that i used for the minimization step ... A structure is only minimized if you ran EM, or the program

Re: [gmx-users] Simulating a particle surface for interaction

Nice! Thank you! Muhammad Naqvi wrote: Hi all, Wonderful community here! FAQs andManuals on one side, nothing beats the advice of experts. Whoever started this forum, thank you. I am learning a lot. I have a question of my own. I am trying to see the interaction of certain

Re: [gmx-users] how to extract the LJ interaction parameters from the tpr file

On 08/02/10 23:07, Baofu Qiao wrote: Hi Mark, Thanks for your reply! I want to use the pre-saved trajectory. Based on the distance criteria, calculate the Coulomb and LJ interaction. However, I don't know the data structure related with the LJ parameters. Do you have related knowledge? The

[gmx-users] compilation problems orte error

Dear All, I am having problems compiling gromacs 4.0.7 in parallel. I am following the Quick and Dirty Installation instructions on the gromacs webpage. I downloaded the the versions of fftw, OpenMPI and gromacs-4.0.7 following these instructions. Everything seems to compile OK and I get

Re: [gmx-users] compilation problems orte error

Jennifer Williams wrote: Dear All, I am having problems compiling gromacs 4.0.7 in parallel. I am following the Quick and Dirty Installation instructions on the gromacs webpage. I downloaded the the versions of fftw, OpenMPI and gromacs-4.0.7 following these instructions. Everything

Re: [gmx-users] mdrun append problem

Dear Justin Thanks for your reply. I didnot get any fatal error. Since, the mdrun has started (mdrun -s spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o spc_25_eq.trr -e spc_25_eq.edr -g spc_25_eq.log -append yes ), it has created new state.cpi. So I now I cannot verify it. From now, I will

Re: [gmx-users] mdrun append problem

Chandan Choudhury wrote: Dear Justin Thanks for your reply. I didnot get any fatal error. Since, the mdrun has started (mdrun -s spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o spc_25_eq.trr -e spc_25_eq.edr -g spc_25_eq.log -append yes ), it has created new state.cpi. So I now I cannot

Re: [gmx-users] ATP for

Hi Tom!! Thanks for the information. I went through the paper and added the new O3 atom type. One unusual thing I noticed was that the sum of the partial charges on the atoms of AT P at the last column of http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/ATP.prepfile is

Re: [gmx-users] compilation problems orte error

As Justin said give the command line options for mdrun and also check that your mpi environment is running. Better to run a parallel job and check its output. Chadnan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Feb 8, 2010 at 8:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:

Re: [gmx-users] ATP for

Are you sure you added it up correctly? I get a number very close to -4. There is no hydrogen on the gamma phosphate as it was parameterised in this way. If the environment in which your ATP is located suggests that the gamma phosphate should be protonated then you need to use other ATP

Re: [gmx-users] ATP for

Thanks Tom. Some how only the negative charges were being added in spreadsheet. So, I got charge around -12. I am simulating 1QHH. It has ATP in it, the structure of the ligand in the rcsb (http://www.pdb.org/pdb/explore/explore.do?structureId=1QHH) shows ATP with hydrogen. -- Chandan kumar

[gmx-users] '+' and '-' sign in rtp file

I had a simple query regarding the rtp file . What does the '+' and '-' sign indicates in the following dihedral inforamtion: [ dihedrals ] CA C+N+Hbackbone_prop_1 O C+N+Hbackbone_prop_2 -C NCACBbackbone_prop_3 -C NCA C

Re: [gmx-users] '+' and '-' sign in rtp file

Chandan Choudhury wrote: I had a simple query regarding the rtp file . What does the '+' and '-' sign indicates in the following dihedral inforamtion: [ dihedrals ] CA C+N+Hbackbone_prop_1 O C+N+Hbackbone_prop_2 -C NCACB

[gmx-users] Re: segmentation fault with grompp

Ok, here's what i've got: Gromacs version 4.0.5. Both platforms are Linux, icc 10, fftw 3 compile option: ./configure --enable-mpi thanks for your help! Gard Gard Nelson wrote: Hi all, I'm trying to simulate a solvated membrane using Berger's lipids. When I run grompp, i get the following

Re: [gmx-users] Compiling 4.0.7 parallel fails

Users, Thanks for the response. To further clarify I am running rhel5 on a single quad machine. I tried Chandan Choudhury's suggestion and that hello world program doesnt output anything on my machine. Here is what i did: 1. mpicc mpitest.c -o test 2. mpirun -np 2 test I made a slight

Re: [gmx-users] Compiling 4.0.7 parallel fails

On Mon, 2010-02-08 at 13:48 -0500, Matthew L. Danielson wrote: Users, Thanks for the response. To further clarify I am running rhel5 on a single quad machine. I tried Chandan Choudhury's suggestion and that hello world program doesnt output anything on my machine. Here is what i did:

[gmx-users] oxy hemoglobin

Dear gromacs users: I am trying to get the topology file for oxy-hemoglobin. As suggested below in the link below, I am trying to modify my itp or rtp file. http://osdir.com/ml/science.biology.gromacs.user/2006-07/msg00236.html But, if anybody has already constructed rtp file for oxy

[gmx-users] RMSD of Different Simulations

Hello All, I've taken the average peptide structure from two different MD simulations using g_rmsf. Is there a method for calculating the RMSD between those two structures? The only difference between the two peptides is a single residue mutation. Thanks. --Venk

[gmx-users] Re: Lennard-Jones Rdf plot

Justin, This is in response to your mail on this subject. My objective was to do an NPT simulation of a 200 particle fluid using Lennard-Jones parameters only. I also used the atomic number, atomic mass, and Lennard-Jones parameters(sigma in nm and epsilin in KJ/mol) for the oxygen atom, and

Re: [gmx-users] Re: Lennard-Jones Rdf plot

Lum Nforbi wrote: Justin, This is in response to your mail on this subject. My objective was to do an NPT simulation of a 200 particle fluid using Lennard-Jones parameters only. I also used the atomic number, atomic mass, and Lennard-Jones parameters(sigma in nm and epsilin in KJ/mol)

Re: [gmx-users] RMSD of Different Simulations

On 09/02/10 10:20, V Hariharan wrote: Hello All, I've taken the average peptide structure from two different MD simulations using g_rmsf. Is there a method for calculating the RMSD between those two structures? The only difference between the two peptides is a single residue mutation. Thanks.

Re: [gmx-users] Re: segmentation fault with grompp

On 09/02/10 09:04, Justin A. Lemkul wrote: Quoting Gard Nelsongardnersnak...@gmail.com: Ok, here's what i've got: Gromacs version 4.0.5. Both platforms are Linux, icc 10, fftw 3 compile option: ./configure --enable-mpi The vast majority of Gromacs programs (read: anything not called

[gmx-users] Problem - can't set dodecahedrons box

Hi, I'm facing a problem with GROMACS that appears pretty simple, actually. I'm trying to set a dodecahedron box but all I can get is a triclinic box. For that, I'm using the following line: * editconf -f pMHC -bt dodecahedron -o -d 1 * Am I doing something wrong?? Another problem, different

Re: [gmx-users] Problem - can't set dodecahedrons box

Maurício Menegatti Rigo wrote: Hi, I'm facing a problem with GROMACS that appears pretty simple, actually. I'm trying to set a dodecahedron box but all I can get is a triclinic box. For that, I'm using the following line: / editconf -f pMHC -bt dodecahedron -o -d 1 / Am I doing something

Re: [gmx-users] Problem - can't set dodecahedrons box

On 09/02/10 12:12, Maurício Menegatti Rigo wrote: Hi, I'm facing a problem with GROMACS that appears pretty simple, actually. I'm trying to set a dodecahedron box but all I can get is a triclinic box. For that, I'm using the following line: / editconf -f pMHC -bt dodecahedron -o -d 1 / Since

Re: [gmx-users] Problem - can't set dodecahedrons box

Hi,  You can post-process your trajectory using trjconv -pbc mol -ur compact to see the real representation. The real representation is the infinite periodic system; there is no box shape there. For representation of a single unit cell you can take any cut that is consistent with the lattice,