[gmx-users] PTR parameters

Dear GMX users, The protein I am trying to run MD involves several phosphorylated tyrosine residues. How or where can I get the itp/top file (or parameters) for this type of proteins? Any help or comments will be appreciated. SY Yang __ Do You Ya

Re: [gmx-users] water molecules

Beniamino Sciacca wrote: Dear GMX users, Viewing my simulations with VMD I see water molecules that become longer; in fact in the simulation I can see some lines (that are water molecules). Why? Is that a simulation problem or a VMD one? I can't tell from your description. Unless you use tr

[gmx-users] water molecules

Dear GMX users,Viewing my simulations  with VMD I see water molecules that become longer; in fact in the simulation I can see some lines (that are water molecules).Why?Is that a simulation problem or a VMD one? Thank you in advanceBeniamino Sciacca ___ gm

Re: [gmx-users] Gromacs-mpi with Rocks v4.0

So what does config.log tell you? Which test program does not compile? To be honest, I can't tell what's going on in config.log (I've pasted it below). I see a 'failed program' message with respect to confdefs.h , but I saw this during the configuration without mpi enabled (and it worked f

[gmx-users] Re: Re: quality of cluster strucutres (David van der Spoel)

> Mauricio Sica wrote: > > Dear all > > > > I´ve obtained one cluster structure from a protein simulation. Then, as I > > wanted to use this structure as a static model, I checked it with WHAT_IF > > and the result was that as a model is a little poor (a list of bad angles, > > bad distances, probl

[gmx-users] email list archives problem on new web site

FYI - on the new web site, the links to the archives of all of the email lists go to the gmx-announce archives. Jonathan Jonathan Moore, Ph.D. Research and Engineering Sciences - New Products Core R&D The Dow Chemical Company 1702 Building, Office 4E Midland, MI 486

Re: [gmx-users] mdrun error

Mahnam wrote: In God We Trust Hi Dr Biswas Thank you for your guids.Excuse me for many question. I am using a serial version of CPMD. I made cpmdmpi script and corrected the path of cpmd.x ( /root/CPMD-3.11.1/SOURCE/cpmd.x CPMD_inp.run.),but when I run rgmx script , mdrun says: GROMACS aw

[gmx-users] mdrun error

In God We Trust Hi Dr Biswas Thank you for your guids.Excuse me for many question. I am using a serial version of CPMD. I made cpmdmpi script and corrected the path of cpmd.x ( /root/CPMD-3.11.1/SOURCE/cpmd.x  CPMD_inp.run.),but when I run rgmx script , mdrun says:  GROMACS awaits QM-result fo

[gmx-users] Pull code with angle constraints

Dear gromacs gurus I wonder to know if there is some straightforward way to implement angle, dihedral and possibly other constraints to the pull code, beside distance constraints. Any idea would help. Sincerely Vojtech Spiwok --- Ing. Vojtech Spiwok, PhD. De

Re: [gmx-users] GROMACS SGI Error

Akshay Patny wrote: Hi I am trying to install GROMACS 3.3.1 on SGI Irix 6.5.20m. I installed and used fftw-3.1.1 during the compiling of gromacs. After I configure using ./configure –prefix=/usr/people/guest/gromacs I did make and got the following error __

Re: [gmx-users] Gromacs-mpi with Rocks v4.0

Arneh Babakhani wrote: Hi Francisco, was wondering if you ever resolved this issue? I too am trying to install gromacs mpi on our cluster, but have had no luck. I get the following error in the configure step: [EMAIL PROTECTED] gromacs-3.3.1]$ ./configure --enable-mpi --prefix=/home/ababakh

Re: [gmx-users] adding new residue (MSE) in topology database

[EMAIL PROTECTED] wrote: hello, I am trying to add Selenomethionine (MSE) residue in to the topology database. And I have to calculate the van der waals parameters V(c6) and W(c12) as they have to be mentioned in ff???nb.itp, for which I have to get the sigma and epsilon values. Where can I fin

[gmx-users] adding new residue (MSE) in topology database

hello, I am trying to add Selenomethionine (MSE) residue in to the topology database. And I have to calculate the van der waals parameters V(c6) and W(c12) as they have to be mentioned in ff???nb.itp, for which I have to get the sigma and epsilon values. Where can I find these valuse or how can

[gmx-users] adding new residue (MSE) in topology database

hello, I am trying to add Selenomethionine (MSE) residue in to the topology database. And I have to calculate the van der waals parameters V(c6) and W(c12) as they have to be mentioned in ff???nb.itp, for which I have to get the sigma and epsilon values. Where can I find these valuse or how can I

[gmx-users] adding new residue (MSE) in topology database

hello, I am trying to add Selenomethionine (MSE) residue in to the topology database. And I have to calculate the van der waals parameters V(c6) and W(c12) as they have to be mentioned in ff???nb.itp, for which I have to get the sigma and epsilon values. Where can I find these valuse or how can I