Re: [gmx-users] lost ngmx

On 29/10/2011 3:51 AM, Victor wrote: Hello gmx-users I have compiled gromacs on Debian/Linux wiht the option --with-x but the ngmx binary has not been generated. I don´t have gnome or kde installed, but I have installed xserver-xorg and I can export VMD with ssh. You probably need more tha

Re: [gmx-users] How to change moment of inertia of a molecule

On 29/10/2011 9:04 AM, Rini Gupta wrote: Dear Gromacs Users, I want to run a calculation using Gromacs for some mixed/water solutions by changing moment of inertia of molecules. Can anyone please tell me is there any one of changing the actual moment of inertia of a molecule e.g. water You w

[gmx-users] How to change moment of inertia of a molecule

Dear Gromacs Users, I want to run a calculation using Gromacs for some mixed/water solutions by changing moment of inertia of molecules. Can anyone please tell me is there any one of changing the actual moment of inertia of a molecule e.g. water Any comments will be really appreciated. Thanks a

Re: [gmx-users] pdb2gmx problem with ACE N-cap

Sanku M wrote: Hi, I have a protein pdb file with ACE as N-cap and I am trying to use pdb2gmx ( within gromacs 4.5.4 ) to generate a topology file using opls/AA . the ACE is present in opls aminoacids.rtp files. But, on issuing the pdb2gmx command, I get following error message: Program

[gmx-users] pdb2gmx problem with ACE N-cap

Hi,   I have a protein pdb file with ACE as N-cap and I am trying to use pdb2gmx ( within gromacs 4.5.4 ) to generate a topology file using opls/AA . the ACE is present in opls aminoacids.rtp files. But, on issuing the pdb2gmx command, I get following error message: Program pdb2gmx_44, VERSION

Re: [gmx-users] Parametrisation of the heteroatomic pdb

James Starlight wrote: Justin? So As I understood the aminoacids.rtp of current force field must include topology for such caps. Yes. Any residue whatsoever that you wish to process with pdb2gmx must be present in an .rtp file. But for example If I have only topology on such groups fo

Re: [gmx-users] Parametrisation of the heteroatomic pdb

Justin? So As I understood the aminoacids.rtp of current force field must include topology for such caps. But for example If I have only topology on such groups for another ff could I include it to the amber FF? If no where I could find such topology ? James 2011/10/28 Justin A. Lemkul > > >

Re: [gmx-users] Parametrisation of the heteroatomic pdb

James Starlight wrote: I understood that but how I can add that groups to termi of the bowh of my chains ? I've tried by -ter but pdb2gmx didnt ask me for the addition of the CAPS. May be Amber ff didnt support this feature ? pdb2gmx does not build things that aren't there. Your input

Re: [gmx-users] file.itp for separated molecules

Fahimeh Baftizadeh wrote: Hello I have to question. 1- I am generating a gro and toplogy file from a pdb file, usign pdb2gmx. the pdb file contains 18 separate chains, in each chain, there are 6 residues. When I generate the topology and coordinates, it creates

Re: [gmx-users] Re: Hbonds - Res - Ligand

Steven Neumann wrote: Hi Justin, Do you have any clue of this problem? You are the last hope, please help :) Sorry, I have no idea. If I did, I would have posted earlier. In principle, PBC re-imaging should not affect the calculation of distances and angles needed by g_hbond and I hav

Re: [gmx-users] extending umbrella sampling runs

Poojari, Chetan wrote: Hi, I want to extend the umbrella sampling runs and have used the below commands: 1) grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n index.ndx -o umbrella0.tpr 2) mdrun -s umbrella0.tpr -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -cpo 0.cpt -

[gmx-users] lost ngmx

Hello gmx-users I have compiled gromacs on Debian/Linux wiht the option --with-x but the ngmx binary has not been generated. I don´t have gnome or kde installed, but I have installed xserver-xorg and I can export VMD with ssh. Do I need to install gnome or kde? if the answer is yes, Do I need

Re: [gmx-users] query on OPLS-2005

Hi Cara,    Thanks for a  very clarifying email. It helps a lot. Sanku From: Cara Kreck To: gmx-users@gromacs.org Sent: Friday, October 28, 2011 3:50 AM Subject: RE: [gmx-users] query on OPLS-2005 Hi Sanku According to the Schrodinger Knowledge Base, this

Re: [gmx-users] Parametrisation of the heteroatomic pdb

I understood that but how I can add that groups to termi of the bowh of my chains ? I've tried by -ter but pdb2gmx didnt ask me for the addition of the CAPS. May be Amber ff didnt support this feature ? James > > You have to build capping groups onto the termini. See, for instance the > [ACE]

[gmx-users] file.itp for separated molecules

Hello > > I have to question. > 1- I am generating a gro and toplogy file from a pdb file, usign pdb2gmx. > the pdb file contains 18 separate chains, in each chain, there are 6 > residues. > When I generate the topology and coordinates, it creates 18 > posres-protein$i.itp file and 18 topol-protein

[gmx-users] extending umbrella sampling runs

Hi, I want to extend the umbrella sampling runs and have used the below commands: 1) grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n index.ndx -o umbrella0.tpr 2) mdrun -s umbrella0.tpr -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -cpo 0.cpt -c 0.gro -x 0.xtc -g 0.log

[gmx-users] Re: Hbonds - Res - Ligand

Hi Justin, Do you have any clue of this problem? You are the last hope, please help :) Steven On Fri, Oct 28, 2011 at 2:45 PM, Steven Neumann wrote: > With other residues is the same... and changes are bigger. Which trajectory > in this case is reliable? > > My wsteps in trjconv involves: > > >

Re: [gmx-users] Parametrisation of the heteroatomic pdb

James Starlight wrote: Justin, hello! I've found that D and L-isomers must be topological identicaly so I've used topology of Leu and Val residues for Dle and Dva resp. I've added information about topology of that two residues to the .rtp .hdb of my force field as well as to the

[gmx-users] umbrella sampling

You need to evaluate convergence yourself for any simulation. I suggest doing the whole thing twice (or more) with different starting conformations. Also, look at the PMF from block averaging (generate one PMF from the 0-2 ns data, another from the 2-4 ns data, and so on) and see if there i

Re: [gmx-users] trjconv and -pbc

Hi Lina, You first remove the jumps from the trajectory. Then you can view that trajectory with ngmx or with VMD. You can also then extract the frames around the 'jump' and look at them. But if the molecule goes unstuck and then crosses the boundary to get stuck to the protein again, it would give

[gmx-users] Re: Hbonds - Res - Ligand

With other residues is the same... and changes are bigger. Which trajectory in this case is reliable? My wsteps in trjconv involves: 1. First make your molecules whole if you want them whole (system). 3. Extract the first frame from the trajectory as reference for removing jumps if

[gmx-users] Re: umbrella sampling

Hi Justin, Here is my complete code for umbrella sampling title = Umbrella pulling simulation define = -DPOSRES_2 integrator = md dt = 0.002 tinit = 0 nsteps = 250 ; 5 ns nstcomm = 10 nstxout = 5 ; every 100 ps nstvout = 5 nstfout

[gmx-users] Hbonds - Res - Ligand

Dear Gmx Users, I have compared average number of hbonds per time frame between my ligand and protein: 1) Using trajectory obtained straight after simulations: g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num 91withLigandsHbond.xvg Avergage number of hbonds: 0.146 2) Using trajectory modifi

Re: [gmx-users] Parametrisation of the heteroatomic pdb

Justin, hello! I've found that D and L-isomers must be topological identicaly so I've used topology of Leu and Val residues for Dle and Dva resp. I've added information about topology of that two residues to the .rtp .hdb of my force field as well as to the

[gmx-users] extending umbrella sampling runs

Hi, I want to extend the umbrella sampling runs and have used the below commands: 1) grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n index.ndx -o umbrella0.tpr 2) mdrun -s umbrella0.tpr -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -cpo 0.cpt -c 0.gro -x 0.xtc -g 0.log -

Re: [gmx-users] umbrella sampling

Vijayaraj wrote: Hello, I am doing umbrella sampling to calculate PMF curve for the detachment of a terminal cyclic peptide with 8 aa's (CP) from the self-assembled cyclic peptide nanotube. I extracted the reaction coordinates staring from 5.5 ang COM distance between the terminal CP and th

Re: [gmx-users] Parametrisation of the heteroatomic pdb

James Starlight wrote: Dear Gromacs users! I've forced with some problem of preparing topology of my input pdb via pdb2gmx. My input structure( gramicidin ion chanell) consist of some heteroatoms due to the presence of the non standart aminoacids in sequence: FOR, DLE, DVA, ETA ( this the

[gmx-users] umbrella sampling

Hello, I am doing umbrella sampling to calculate PMF curve for the detachment of a terminal cyclic peptide with 8 aa's (CP) from the self-assembled cyclic peptide nanotube. I extracted the reaction coordinates staring from 5.5 ang COM distance between the terminal CP and the 2nd CP to 17.5 ang, I

Re: [gmx-users] trjconv and -pbc

On Fri, Oct 28, 2011 at 5:37 PM, Tsjerk Wassenaar wrote: > Hi Lina, > > My previous reply was from before I looked at the graph. Have you > considered that the molecule might be taking a stroll and turn back, Ha ... stroll?! > or goes to another side of the protein? Have you looked at the > trajec

[gmx-users] Parametrisation of the heteroatomic pdb

Dear Gromacs users! I've forced with some problem of preparing topology of my input pdb via pdb2gmx. My input structure( gramicidin ion chanell) consist of some heteroatoms due to the presence of the non standart aminoacids in sequence: FOR, DLE, DVA, ETA ( this the R isomers instad of L analogs)

Re: [gmx-users] trjconv and -pbc

Hi Lina, My previous reply was from before I looked at the graph. Have you considered that the molecule might be taking a stroll and turn back, or goes to another side of the protein? Have you looked at the trajectory, in particular at the trajectory with the jumps removed? Cheers, Tsjerk On Fr

RE: [gmx-users] query on OPLS-2005

Hi Sanku According to the Schrodinger Knowledge Base, this is the paper that should be referenced for OPLS-2005 instead: Banks, J.L., H.S. Beard, Y. Cao, A.E. Cho, W. Damm, R. Farid, A.K. Felts,T.A. Halgren, D.T. Mainz, J.R. Maple, R. Murphy, D.M. Philipp, M.P. Repasky,L.Y. Zhang, B.J. Bern

Re: [gmx-users] trjconv and -pbc

Hi Lina, Don't combine fitting, centering and pbc options. It may not work as expected. That's why the workflow is given. Use separate passes. By the way, first centering on the protein followed by putting molecules in the box should also work. Cheers, Tsjerk On Oct 28, 2011 9:01 AM, "lina" wr

Re: [gmx-users] trjconv and -pbc

On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar wrote: > Hi Lina, > > Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump > > Hope it helps, Hi, Thanks. I tried trjconv_g -fit translation -pbc nojump, ideally it should work. but still not, after I tried the minidis