Re: [gmx-users] pdb2gmx error

On 10/7/15 3:01 PM, Dries Van Rompaey wrote: Hi Mark, This is Gromacs 5.0.4. This is a non-terminal residue. The command line used is: gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh) I tried this procedure with and without ignh flag. As far as I know, specbonds is not in play.

Re: [gmx-users] pdb2gmx error

Thanks Justin, that makes sense! I'm wondering why none of the other proline residues triggered that warning though? The same procedure works like a charm with other proteins. On 7 Oct 2015 10:59 pm, "Justin Lemkul" wrote: > > > On 10/7/15 3:01 PM, Dries Van Rompaey wrote: > >>

Re: [gmx-users] pdb2gmx error

On 10/7/15 5:03 PM, Dries Van Rompaey wrote: Thanks Justin, that makes sense! I'm wondering why none of the other proline residues triggered that warning though? The same procedure works like a charm with other proteins. Without access to all of the files you're looking at, the best I can do

Re: [gmx-users] Gromacs

i tried to run in OPLSAA force field sir. *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* On Tue, Oct 6, 2015 at 7:39 PM, Ebert Maximilian wrote: > Maybe you should

[gmx-users] Dftb as qmmm method with gromacs

Hello all, I want to use dftb as a qmmm method with gromacs as explained in a recent research article " http://onlinelibrary.wiley.com/doi/10.1002/jcc.24029/abstract;. When I am trying to compile gromacs-5.0 with dftb using flag " *-DGMX_QMMM_DFTB*", the cmake .. command is terminating with the

Re: [gmx-users] Free Energy of Liquid Water

Thanks for explaining, (and Professor Farais de Moura as well) that makes sense. On a different note, I've noticed a huge difference in performance between my equillibration run and my actual simulation, and I'm wondering if this is normal. For comparison, I ran a couple small (meaningless)

Re: [gmx-users] Free Energy of Liquid Water

If ALL the particles are changing with the free energy coupling parameter, then GROMACS will slow down quite a bit. If only one molecule is changing, then it shouldn't be that much slower (20-30% slower?) But without .mdp and.top files, it's hard to say exactly what is happening. On Wed, Oct

[gmx-users] Virtual sites error

Trying to add hydrogen virtual sites to the model (using -vsites h option in pdb2gmx) results in a salvo of error messages when running grommp to create .tpr file after the solvation: ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]: No default Constr. No Conn. types ERROR 2 [file

Re: [gmx-users] Hydrogen bonding energy calculation (Ben)

Hi Dr. Spoel, Thanks for your reply! I set my script as follows: gmx pdb2gmx -f water.pdb -o water.gro -water tip3p << EOF #water.pdb is a pdb file contains a single water molecule 5 #OPLS 2 #TIP3P EOF gmx editconf -f water.gro -o water_newbox.gro -c -d 1.5 -bt

Re: [gmx-users] GROMACS On GPU

only i need to install from source,or should i install CUDA Toolkit? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

Re: [gmx-users] Gromacs

Hi, How is it possible that you have finished up to production run without the .top file ? The first line of your ebolaag.top says that the topology has been generated. How have you been doing any of the equilibration steps without the .top file? Information regarding atoms are there in the

Re: [gmx-users] Install Gromacs on VirtualBox

Hi, Unfortunately that does not tell much (at least not without a backtrace). You can e.g. run the regressiontests to see whether mdrun does start at all (or just run "gmx mdrun" manually). -- Szilárd On Tue, Oct 6, 2015 at 4:06 PM, Simon Dürr wrote: > Hi Szilard,

Re: [gmx-users] pdb2gmx error

Hi, Is it terminal? Are there specbonds in play? What's the GROMACS version? What's your pdb2gmx command line? :-) Mark On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey wrote: > Hi everyone, > > I'm getting the following warning when I try to run pdb2gmx on my

[gmx-users] pdb2gmx error

Hi everyone, I'm getting the following warning when I try to run pdb2gmx on my protein structure: WARNING: WARNING: Residue 168 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type dihedral in that entry is not

Re: [gmx-users] installing gromacs-5.0.5

i think you should install by downloading source file and CUDA toolkit for your GPU.may i know what is your GPU? i also wondering about GPU and CUDA ? Nikhil -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] GROMACS On GPU

Hi, Check out what the install guide says ;-) Mark On Wed, Oct 7, 2015 at 3:43 PM Nikhil wrote: > only i need to install from source,or should i install CUDA Toolkit? > > -- > Gromacs Users mailing list > > * Please search the archive at >