Re: [gmx-users] GROMOS 54a7 parameters for rare amino acids (eg. beta-alanine)

Hi Mark, I've consulted the GROMACS manual and I'm working on a few things. I feel the explanations provided in the Hydrogen Database setion could be aided with diagrams somehow. I'll have a look into people that have topologies for b-alanine to save myself trying to get the formatting of

Re: [gmx-users] GROMOS 54a7 parameters for rare amino acids (eg. beta-alanine)

Hi Mark, I noticed your paper from 2011 on parameter optimisation using EWALD and your position and GROMACS so I feel humbled to be talking with you. I have had a 'guess' at the topology for b-alanine (BAL) and added it to my aminoacids.rtp file in the gromos forcefield directory that I am

Re: [gmx-users] Gromacs Orca QMMM segfault

Hi, Yes that's pretty likely, given the lack of maintenance on this feature. Mark On Thu, 23 Jun 2016 23:40 Thilo Mast wrote: > Okay, I've found the problem. > I think there is a problem between the communication of Gromacs v5.x and > ORCA. > When I use Gromacs v4.6.7 it

Re: [gmx-users] Gromacs Orca QMMM segfault

Okay, I've found the problem. I think there is a problem between the communication of Gromacs v5.x and ORCA. When I use Gromacs v4.6.7 it works ... Am 23.06.2016 um 15:29 schrieb Thilo Mast: Hi GMX users, I'm trying to run a QM/MM simulation with Gromacs v5.0 and ORCA v3.0.1. The energy

[gmx-users] Gromacs Orca QMMM segfault

Hi GMX users, I'm trying to run a QM/MM simulation with Gromacs v5.0 and ORCA v3.0.1. The energy minimization of my system works! However, when I try to start the MD simulation with mdrun_d -nt 1 -deffnm nvt I get the following error: Layer 0 nr of QM atoms 51 QMlevel: RHF/3-21G* Setting

Re: [gmx-users] How to manage carbohydrate connected to a protein

On 6/23/16 10:15 AM, Stella Maganhi wrote: Hi Gromacs users!!! I would like to know how to run a protein covalently bonded to a carbohydrate in gromacs using CHARMM. The carb is covalently bonded to an aminoacid side chain. Use the CHARMM-GUI web interface. It will construct the entire

Re: [gmx-users] Does gmx covar/gmx anaeig give or T for ligand binding?

On 22/06/16 08:22, Billy Williams-Noonan wrote: Yes, still with two ligands... So I assume that should be halved to about -0.25 kJ/mol K, which would give T= -75. I found out recently that we have access to a node with 1TB of RAM. So the solvent is still relevant? If the amount of memory I

Re: [gmx-users] Energy minimization has stopped

Thanks a lot Justinn and Mark for the valuable suggestions. I will start over again by choosing a force field which is suitable for the RNA molecules. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun

Re: [gmx-users] Energy minimization has stopped

On 6/23/16 7:17 AM, Anurag Dobhal wrote: Dear Justin, The main aim of the study is to study the interaction between a polymer (chitosan) and RNA molecules by simulating them togather. I have already successfully simulated my polymer system using OPLS AA force field. To simulate them together

Re: [gmx-users] Energy minimization has stopped

Hi, You were recommended to pick a force field, not to combine parts of force fields. Choosing to simulate your polymer OPLS/AA if you then want to combine with RNA is not a good experimental design, unless you can do the combined simulation also in OPLS/AA. I would repeat the polymer experiment

Re: [gmx-users] Energy minimization has stopped

Dear Justin, The main aim of the study is to study the interaction between a polymer (chitosan) and RNA molecules by simulating them togather. I have already successfully simulated my polymer system using OPLS AA force field. To simulate them together I need to write the OPLS AA parameters for

Re: [gmx-users] Energy minimization has stopped

On 6/23/16 7:00 AM, Anurag Dobhal wrote: I am using OPLS AA force field. parameters (charges) for the atoms are taken from the charmm27 force field. So, by using some hybridized force field, you can't successfully minimize a structure. That should tell you something. Why are you trying

Re: [gmx-users] Energy minimization has stopped

I am using OPLS AA force field. parameters (charges) for the atoms are taken from the charmm27 force field. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul

Re: [gmx-users] Energy minimization has stopped

On 6/23/16 6:44 AM, Justin Lemkul wrote: On 6/23/16 6:35 AM, Anurag Dobhal wrote: Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force field. I have written parameters using CHARMM27 force field for RNA molecules. What does this mean? Are you using OPLS-AA or

Re: [gmx-users] Energy minimization has stopped

On 6/23/16 6:35 AM, Anurag Dobhal wrote: Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force field. I have written parameters using CHARMM27 force field for RNA molecules. What does this mean? Are you using OPLS-AA or CHARMM27? Minimising the molecule by invoking

[gmx-users] Energy minimization has stopped

Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force field. I have written parameters using CHARMM27 force field for RNA molecules. Minimising the molecule by invoking mdrun gives me the follwoing error. Energy minimization has stopped, but the forces have not converged to the

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, That depends how your mpi is implemented, but what you really want is a filesystem visible on each node. But since mpirun gmx_mpi mdrun is working, then it's fine. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] How does gromacs checkpoint works

Hi Mark, Thank you very much! Regards, Husen On Thu, Jun 23, 2016 at 3:42 PM, Mark Abraham wrote: > Yes > > On Thu, Jun 23, 2016 at 9:54 AM Husen R wrote: > > > Hi, > > > > Could you tell me the location of the code ? > > is this the location of

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, I'm wondering, if I use gromacs in cluster environment, do I have to install gromacs in every nodes (at /usr/local/gromacs in every nodes) ? or is it enough to install gromacs in one node (example,in head-node) only ? Regards, Husen On Thu, Jun 23, 2016 at 3:41 PM, Mark Abraham

Re: [gmx-users] How does gromacs checkpoint works

Yes On Thu, Jun 23, 2016 at 9:54 AM Husen R wrote: > Hi, > > Could you tell me the location of the code ? > is this the location of the code -> > gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp ? > > regards, > > Husen > > On Thu, Jun 23, 2016 at 2:23 PM, Mark Abraham

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, The only explanation is that that file is not in fact properly accessible if rank 0 is placed other than on "compute-node," which means your organization of file system / slurm / etc. aren't good enough for what you're doing. Mark On Thu, Jun 23, 2016 at 10:15 AM Husen R

Re: [gmx-users] restart error

Great thank you! On 2016-06-23 09:39, Mark Abraham wrote: Hi, There's two possibilities here. 1) GROMACS has a bug with multi-simulation checkpointing - several people are reporting problems, and it's probably getting an overhaul for the 2016 release because it was far from clear the old

Re: [gmx-users] GROMOS 54a7 parameters for rare amino acids

Otherwise you may try your luck with the ATB server for Gromos topologies: https://atb.uq.edu.au Gerrit Hi, There's a collection of contributed stuff on the GROMACS webpage, so good luck with that... But mostly it's a matter of people choosing to share. Authors of papers where such have been

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, I still unable to find out the cause of the fatal error. Previously, gromacs is installed in every nodes. That's the cause Build time mismatch and Build user mismatch appeared. Now, Build time mismatch and Build user mismatch issues are solved by installing Gromacs in shared directory. I

Re: [gmx-users] selection of start or end terminus

Dear Alex, A single amino acid is not a peptide sine it has no peptide bonds. Kind regards, Erik > On 22 Jun 2016, at 20:19, Alexander Alexander > wrote: > > Thanks for your response. > > And then why does "1" go wrong for a single amino acid in zwitterions >

Re: [gmx-users] How does gromacs checkpoint works

Hi, Could you tell me the location of the code ? is this the location of the code -> gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp ? regards, Husen On Thu, Jun 23, 2016 at 2:23 PM, Mark Abraham wrote: > Hi, > > There's only the code. All you have to do is write

Re: [gmx-users] GROMOS 54a7 parameters for rare amino acids (eg. beta-alanine)

Hi, There's a collection of contributed stuff on the GROMACS webpage, so good luck with that... But mostly it's a matter of people choosing to share. Authors of papers where such have been used should be willing to share topology files. Mark On Thu, Jun 23, 2016 at 8:08 AM Billy Williams-Noonan

Re: [gmx-users] least-squares fitting the second structure on the reference structure

Hi, Each frame of the trajectory is fitted to the reference structure independently of the others... but not if you're using gmx confrms, which only acts on a single frame anyway... Mark On Thu, Jun 23, 2016 at 12:11 AM Qasim Pars wrote: > Hi Tsjerk, > > Thanks, I know

Re: [gmx-users] restart error

Hi, There's two possibilities here. 1) GROMACS has a bug with multi-simulation checkpointing - several people are reporting problems, and it's probably getting an overhaul for the 2016 release because it was far from clear the old version was always working 2) Your (parallel) file system isn't

Re: [gmx-users] How does gromacs checkpoint works

Hi, There's only the code. All you have to do is write down everything that you were going to need to read to do the next step (unless it's from the .tpr). Add some checksums of the last pieces of output files, so you can help the user not mangle their files upon restart. Decide how you're going

[gmx-users] Relative FEP with restraints

Dear gmx-users, I have performed a relative FEP simulation involving a small mutation to my ligand. In order to prevent distortions to the protein structure I added harmonic position restraints to the protein backbone. Does anyone have a reference article for the correct treatment of the

[gmx-users] GROMOS 54a7 parameters for rare amino acids (eg. beta-alanine)

Hi Gromacs Users, Does anyone know where I can find a set of download-able parameters for rare amino acids? Is there a repository of some kind? Kind regards, Billy -- Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon *LinkedIn Profile