[gmx-users] where is the script?

Hello: I found that someone mentioned that there is a script from Mark which could be used to convert CGenff format into Gromacs .itp file. I searched the mailist and didn't find it. I am just wondering where can I obtain this script? thank you very much best Albert -- gmx-users mailing

[gmx-users] Re: energy-mimisation-problem

On Sun, Nov 25, 2012 at 9:08 PM, SANTU BISWAS santu.biswa...@gmail.com wrote: dear users, When performing a energy minimization of a polypeptide(formed by lysine-5-residues) in vacuum box by using Steepest Descent and also Conjugate Gradient methods in gromacs double

Re: [gmx-users] where is the script?

On 2012-11-26 12:00, Albert wrote: Hello: I found that someone mentioned that there is a script from Mark which could be used to convert CGenff format into Gromacs .itp file. I searched the mailist and didn't find it. I am just wondering where can I obtain this script? thank you very much

[gmx-users] Re: force vs time plot

This should be in the pullf.xvg (time and then the forces). Am 24.11.2012 19:55, schrieb gmx-users-requ...@gromacs.org: Hi to all gromacs users, I am trying to run an umbrella sampling and i am getting the initial conformations by pulling simulations but i want to check the simulation

Re: [gmx-users] GPU warnings

On Sun, Nov 25, 2012 at 8:47 PM, Thomas Evangelidis teva...@gmail.comwrote: Hi Szilárd, I was able to run code compiled with icc 13 on Fedora 17, but as I don't have Intel Compiler v13 on this machine I can't check it now. Please check if it works for you with gcc 4.7.2 (which is the

Re: [gmx-users] Is any command to distinguish gromacs 4.5.4 and 4.5.5

Or run any binary with the -version option e.g: $ mdrun -version -- Szilárd On Sun, Nov 25, 2012 at 10:30 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Look at the top of the output of any GROMACS program. Mark On Sun, Nov 25, 2012 at 10:06 AM, Acoot Brett acootbr...@yahoo.com wrote:

Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

On 11/26/12 12:58 AM, Venkat Reddy wrote: Dear all, I am simulating a Protein-Drug complex. I am following Justin's tutorial. I have used *PRODRG *for generating topology. *Gaussian *has given me the ESP charges. I have edited the charges in the itp file using the *Gaussian*'s ESP charges*.

Re: [gmx-users] Re: energy-mimisation-problem

On 11/26/12 6:01 AM, SANTU BISWAS wrote: On Sun, Nov 25, 2012 at 9:08 PM, SANTU BISWAS santu.biswa...@gmail.com wrote: dear users, When performing a energy minimization of a polypeptide(formed by lysine-5-residues) in vacuum box by using Steepest Descent and also Conjugate

Re: [gmx-users] Umbrella sampling - regd

On 11/26/12 1:03 AM, ramesh cheerla wrote: Dear Gromacs users, I am calculating PMF for the ion permeation through a tunnel, using umbrella sampling. In my system I have some binding sites with ions, I have removed some ions from binding sites before pulling and In pulling simulations

Re: [gmx-users] where is the script?

On 11/26/2012 02:36 PM, David van der Spoel wrote: It's posted on the website. http://www.gromacs.org/Downloads/User_contributions/Other_software You want this one:charmm2gromacs-pvm.py -- thanks a lot for kind reply. But how to use it? I am trying to run with command: python

Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

Dear Justin, I haven't touched the *Mass column.* I have edited the charges only using gedit in linux. On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 12:58 AM, Venkat Reddy wrote: Dear all, I am simulating a Protein-Drug complex. I am following Justin's

Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

On 11/26/12 9:12 AM, Venkat Reddy wrote: Dear Justin, I haven't touched the *Mass column.* I have edited the charges only using gedit in linux. Regardless, the masses I pointed out are wrong. You should still do the test to #include the original topology and see if it works, then if it

Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

Thanks Justin...I will certainly do. On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 9:12 AM, Venkat Reddy wrote: Dear Justin, I haven't touched the *Mass column.* I have edited the charges only using gedit in linux. Regardless, the masses I pointed

Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

Dear Justin, One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I mix 53A6 and 43A1? On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 9:12 AM, Venkat Reddy wrote:

Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

On 11/26/12 9:35 AM, Venkat Reddy wrote: Dear Justin, One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I mix 53A6 and 43A1? PRODRG doesn't even do a very good job of being compatible with 43A1, so

Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

Thank yo Justin for your help...I have generated the same topology using *ATB. *Now, I got the masses correctly (as pointed out by you). So, I'm afraid that is there any bug in PRODRG server? On Mon, Nov 26, 2012 at 8:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 9:35 AM, Venkat

Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

On 11/26/12 9:43 AM, Venkat Reddy wrote: Thank yo Justin for your help...I have generated the same topology using *ATB. *Now, I got the masses correctly (as pointed out by you). So, I'm afraid that is there any bug in PRODRG server? I have no idea. I haven't used PRODRG in a very long

[gmx-users] maxwell-boltzmann distribution

Hi dear GROMACS experts I wanna know if GROMACS uses only Maxwell-Boltzmann distribution in statistical mechanics, or it also uses Fermi-Dirac and Bose-Einstein statistics.If it only uses Maxwell-Boltzmann distribution, are the results reliable and correct? I mean can we use this law, which is

[gmx-users] Installation problems with MacOS 10.7.5

Dear Users, I have problems with the installation of GROMACS 4.5.5 on MacOS 10.7.5. GCC version 4.2.1 FFTW is: FFTW-3.3.2. The CMAke command cmake -DGMX_THREAD_MPI=OFF \ -DFFTW3F_INCLUDE_DIR=$FFTWDIR/include \ -DFFTW3F_LIBRARIES=$FFTWDIR/lib \

[gmx-users] g_select error

hello: I am going to calculate the number of water molecules within 6 A of residue 114 by following command: g_select -f md.xtc -s npt3.pdb -os size.xvg -select resid 114 and rdist 0.6 but it said: WARNING: masses and atomic (Van der Waals) radii will be determined based on

Re: [gmx-users] Umbrella sampling - regd

Dear Justin, I am very thankful to you for your reply, you are correct, I have plotted the histo.xvg file in wrong manner. After plotting histograms in correct manner I have realized that my sampling is very poor as histograms and there overlapping is restricted to some regions only, no

Re: [gmx-users] Bonds - force constant for given Beads

the distance distribution should be given by the Boltzmann factor of the potential energy function between the beads, assigning V(r)=0 for the most probable distance in your histogram. that's what you get when you take a molecule in vacuum and for instance you compare the dihedral distribution

Re: [gmx-users] Installation problems with MacOS 10.7.5

You need to name libraries with FFTW3F_LIBRARIES, not the library path. That explains the dropped dependency and subsequent problems. Mark On Mon, Nov 26, 2012 at 4:19 PM, Stefan Jasconek stjas...@students.uni-mainz.de wrote: Dear Users, I have problems with the installation of GROMACS 4.5.5

[gmx-users] g_select error

hello: I am going to calculate the number of water molecules within 6 A of residue 114 by following command: g_select -f md.xtc -s npt3.pdb -os size.xvg -select resid 114 and rdist 0.6 but it said: WARNING: masses and atomic (Van der Waals) radii will be determined based on

[gmx-users] Re: Bonds - force constant for given Beads

A good start might be: Phys. Chem. Chem. Phys., 2011, 13, 10437–10448 This paper is about hybrid-models (mixing CG and AA). But they discuss 'boltzmann inversion' and 'force matching', which are both methods to obtain CG-potentials. Since they use small molecules it focusses on nonbonded

Re: [gmx-users] How to avoid adding ions close to ligand

On 2012-11-26 21:28, Yun Shi wrote: Hi everyone, I am doing conventional MD of a protein-ligand system with a mobile loop as part of the binding site. Presumably, the positive Arg side chain on the mobile loop will eventually move towards the negative carboxylic group on my ligand. But I found

Re: [gmx-users] g_select error

On 11/26/12 2:08 PM, Albert wrote: hello: I am going to calculate the number of water molecules within 6 A of residue 114 by following command: g_select -f md.xtc -s npt3.pdb -os size.xvg -select resid 114 and rdist 0.6 but it said: WARNING: masses and atomic (Van der Waals) radii

Re: [gmx-users] How to avoid adding ions close to ligand

I did hope the ions will move out eventually. But after my ~70ns of conventional MD (with duplicate MD runs and the protein as a dimer with identical sequence), they were still there in the binding site. So I assume it would be much better to start without any salt ions beside my ligand. Could

Re: [gmx-users] How to avoid adding ions close to ligand

There is nothing stopping you from replacing the ion in your binding pocket with the original water and then replacing another water elsewhere with the ion at the oxygen's coordintes, then running genconf to renumber the gro file. On 2012-11-26 06:25:47PM -0800, Yun Shi wrote: I did hope the

[gmx-users] itp atomtypes section

Dear users, I apologise if this is a stupid question, however after a morning of searching I have not been able to find the answer. 1. I have a sample itp file and it contains a section like this: [ atomtypes ] CF CF 6 12.011000.2588 A3.5e-01 2.56134e-01 HF

[gmx-users] Validation of topology ....

Dear Gromacs friends, I want to simulate a system containing the biotin. I get the topology from ATB. I want to validate these toplogy for my use . So please could some one told me the way how I can do it ?? I never had any such experience. Is these is any tutorial regarding to these.