Re: [gmx-users] Dynamics of the salt-bridges

Justin, I suppose that the ussage of the sub-set of trajectories is suitable when you've already known possible salt-bridge pairs. But that time I'd like to obtain that information from my trajectory. E.g I have membrane-embedded protein which is the buddle of alpha-helixes. I want to examine dyna

Re: [gmx-users] BAR histogram results

On 2/1/13 6:07 PM, Sonia Aguilera wrote: Hi! I just finished a FE calculation using the BAR method. This is the plot of my histogram.xvg file: It is my understanding that data must be overlaped in order to get adequate sampling

Re: [gmx-users] Re: question about fftw3 in gromacs 4.6 installation

On 2/1/13 5:26 PM, didymos wrote: Hi Justin! I had the same problem and I used your advise but I am not sure if this entirely worked for me... I used: cmake -DGMX_MPI=ON DCMAKE_INSTALL_PREFIX=$HOME/gromacs -DFFTWF_INCLUDE_DIR=$HOME/fftw/include -DFFTWF_LIBRARY=$HOME/fftw/lib/libfftw3f.so -DCM

[gmx-users] BAR histogram results

Hi! I just finished a FE calculation using the BAR method. This is the plot of my histogram.xvg file: It is my understanding that data must be overlaped in order to get adequate sampling (I have been following Justin Lemkul's tuto

[gmx-users] Re: question about fftw3 in gromacs 4.6 installation

Hi Justin! I had the same problem and I used your advise but I am not sure if this entirely worked for me... I used: cmake -DGMX_MPI=ON DCMAKE_INSTALL_PREFIX=$HOME/gromacs -DFFTWF_INCLUDE_DIR=$HOME/fftw/include -DFFTWF_LIBRARY=$HOME/fftw/lib/libfftw3f.so -DCMAKE_PREFIX_PATH=$HOME/fftw/ .. and I

Re: [gmx-users] Dynamics of the salt-bridges

On 2/1/13 3:22 PM, James Starlight wrote: Dear Gromacs users! I have trajectory from which I want to investigate dynamics of all possible salt bridges (E.g distance between adjacent + and - charged residues) of my protein during the simulation As I understood ussage of g_saltbr -t -sep could

[gmx-users] Dynamics of the salt-bridges

Dear Gromacs users! I have trajectory from which I want to investigate dynamics of all possible salt bridges (E.g distance between adjacent + and - charged residues) of my protein during the simulation As I understood ussage of g_saltbr -t -sep could be suitable for such thing but I'm not sure i

Re: [gmx-users] C instead of CH2 in alkane chain with PRODRG

On 2/1/13 11:47 AM, Stephan Gekle wrote: Dear all, I want to produce a perylene with a connected alkane chain using PRODRG. I draw the molecule using JME, run it through PRODRG. Then some of the polar hydrogens connected to the C rings are missing. But the alkane chains have the correct uni

Re: [gmx-users] get the center of a cluster using gromacs

On 2013-02-01 16:14, Houcemeddine Othman wrote: Hi, I used this command g_cluster -f input.pdb -s input.pdb -cl output.pdb -nofit -av I got a file containing all the structures of the cluster. I am not sure if the first one is the cluster center? It says in the cluster.log file. Houcemeddin

Re: [gmx-users] Error in BlueGene

Hello Ricardo, I tried to decrease the integration time but I got the same error. The system is running fine in my local core. I have two questions: 1) What do you mean by "I balance the domain decomposition for the larger number of core"? 2) Are you running simulations at Bluegene P at Rice

[gmx-users] C instead of CH2 in alkane chain with PRODRG

Dear all, I want to produce a perylene with a connected alkane chain using PRODRG. I draw the molecule using JME, run it through PRODRG. Then some of the polar hydrogens connected to the C rings are missing. But the alkane chains have the correct united atom type (CH2/CH3). Following another

Re: [gmx-users] ligand topology error

On 2/1/13 9:37 AM, az kalsom wrote: hi, whenever, i Submit the molecule to ATB ( http://compbio.biosci.uq.edu.au/atb/index.py) FOR BUILDING THE TOPOLOGY OF LIGAND, IT SAYS Your job that was submitted at 2013-02-01 00:56:07 (RNME = _NGD) had at least one error. Specifically, the QM calculation

[gmx-users] Derive the heme charge

Hello, I want to derive the atomic partial charges for heme in chloroperoxidase, since these parameters cannot be found in the GROMOS53a6 force field. Chloroperoxidase is a cysteine-ligated heme protein (high spin) much like P450. In my work, I want to study the interactions between the protein re

Re: [gmx-users] get the center of a cluster using gromacs

Hi, I used this command g_cluster -f input.pdb -s input.pdb -cl output.pdb -nofit -av I got a file containing all the structures of the cluster. I am not sure if the first one is the cluster center? Houcemeddine On Mon, Jan 28, 2013 at 9:49 AM, francesco oteri wrote: > Hi, > you can try using

Re: [gmx-users] gromacs 4.6 installation error

Hi, make sure to run source /opt/intel/bin/iccvars.sh intel64 before compiling. Roland On Fri, Feb 1, 2013 at 9:06 AM, Fernando Favela wrote: > Hi justin, > > this is the other error message: > [ 56%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall.c.o > [ 56%] [ 56%] [ 56%] Bui

[gmx-users] ligand topology error

hi, whenever, i Submit the molecule to ATB ( http://compbio.biosci.uq.edu.au/atb/index.py) FOR BUILDING THE TOPOLOGY OF LIGAND, IT SAYS Your job that was submitted at 2013-02-01 00:56:07 (RNME = _NGD) had at least one error. Specifically, the QM calculation failed. The most likely cause is that e

Re: [gmx-users] gromacs 4.6 installation error

Hi justin, this is the other error message: [ 56%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall.c.o [ 56%] [ 56%] [ 56%] Building C object src/mdlib/CMakeFiles/md.dir/mvxvf.c.o Building C object src/mdlib/CMakeFiles/md.dir/qm_mopac.c.o Building C object src/mdlib/CMakeFiles/md.di

Re: [gmx-users] gromacs 4.6 installation error

On 2/1/13 8:35 AM, Fernando Favela wrote: Dear Mark Abraham, without the sudo, the problem is still there: ... … ... [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/ewald.c.o [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/calcvir.c.o Linking CXX shared library libmd.so [ 65%] Built

Re: [gmx-users] gromacs 4.6 installation error

Dear Mark Abraham, without the sudo, the problem is still there: ... … ... [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/ewald.c.o [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/calcvir.c.o Linking CXX shared library libmd.so [ 65%] Built target md make: *** [all] Error 2 It could be

Re: [gmx-users] MM-GB/SA analysis in Gromacs

Hi Andrea, Thank you so much for bringing forth the paper. I have performed a MD simulation and would very much like to use the tool mentioned in the paper to calculate the binding free energy. Is it possible for you to kindly give me an access to the same and also a brief explanation as to how to

[gmx-users] Re: MM-GB/SA analysis in Gromacs

Hello dear, I have performed a 50 ns MD simulation of a protein with ligand using gromacs software. I need to do mmpbsa calculation but gromacs don't have this option. I see your paper and your discussion about a script you made to calculate mmpbsa using gromacs trajectory, can you give me access t

[gmx-users] Re: clarification regarding contact map - g_mdmat

Dear users, Sorry. It is because the unit of the cutoff distance ]is in nm. Thank you kavya On Fri, Feb 1, 2013 at 1:28 PM, Kavyashree M wrote: > Dear users, > I used g_mdmap to calculate the C-alpha contact map of > the trajectory. the distance cut off of 8.0 Ang was selected > The protein is

Re: [gmx-users] grimaces 4.6 installation error

On Fri, Feb 1, 2013 at 2:18 AM, Fernando Favela wrote: > Dear Gromacs users, > > I'm trying to install GMX 4.6 in a 64 Bit Machine with Nvidia GTX 680 > cards, I've already installed the intel compilers, cuda 5 and openmpi. > > I do the following procedure: > CC=/opt/intel/bin/icc CXX=/opt/intel/b