Re: [gmx-users] Pro-lig under one molecule type

Ok, Thank you Sir. I am trying to check. On Thu, Feb 18, 2016 at 7:10 PM, Justin Lemkul wrote: > > > On 2/18/16 6:23 AM, Subhashree Rout wrote: > >> Thank you Sir for your suggestions. But sir I am simulating only protein >> in >> water where pdb2gmx itself generates topol.top

[gmx-users] converted topology from amber to gromacs

Hi gromacs users, I've generatedinitial structure of my system by using ambertools (topology andcoordinate files) and converted it to gromacs format (.gro and .top)by parmed, but in topology file it doesn't refer to any forcefield.Does it make any problem in the results or it is ok? Because

[gmx-users] Fragmented backbone

Dear Gromacs users/experts I was doing principal component analysis with a long (1000 ns) MD trajectory. I have seen the protein backbone continuous (not fragmented) with the simulation time. However, the backbone is fragmented in some trajectories corresponding to some of the eigenvectors! The

[gmx-users] how to set Restraints

 hisir Justin Lemkul  and gmx usersi am stuck in a problem. i am performing MD simulation of complex of protein and ligand for binding free energy calculation. i have done all the basics of MD, performed all the BEVANLAB tutorials for my learning and some other papers examples. but i never

Re: [gmx-users] Segmentation fault while using external water model

Hi, I’m not entirely sure. How can I check? Below is my .mdp file (with misleading/old comments): title = OPLS Lysozyme NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps

Re: [gmx-users] Segmentation fault while using external water model

Hi, Are these bonds being converted to constraints, like the original message suggested? Mark On Fri, 19 Feb 2016 02:14 Irem Altan wrote: > Hi, > > I am still having trouble using TIP4P2005. When I start running my MD > simulation, it “runs” for a minute or so (although

[gmx-users] Segmentation fault while using external water model

Hi, I am still having trouble using TIP4P2005. When I start running my MD simulation, it “runs” for a minute or so (although it does not start the simulation itself), and then crashes with a segmentation fault. I have (modified) copy of the amber99sb forcefields in my working directory, and I

[gmx-users] protein transport in nanotube

Hi, Is there any tutorial or available code for simulation of an arbitrary protein transport in a nanotube. I would like to learn how this approach and model/implement this for obtaining diffusion coefficients. Thanks -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Nitrate parameters CHARMM

Hi Tyler, http://dx.doi.org/10.1002/smll.201102056 Best, Thomas From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tyler Cropley [tyler.crop...@wagner.edu] Sent: Thursday, February

[gmx-users] Nitrate parameters CHARMM

Dear Gromacs users, We are trying to set up simulations using the nitrate anion. Unfortunately, the CHARMM force field does not support nitrate. Does anyone know the parameters needed or can point me to a paper that contains them. Thank you! Tyler Cropley -- Gromacs Users mailing list * Please

Re: [gmx-users] tip4p2005 with gromacs 4.6.5

Thanks, I commented out the settles block in tip4p2005cw.itp and it worked! Best, Irem On Feb 18, 2016, at 8:36 AM, Justin Lemkul > wrote: On 2/17/16 6:29 PM, Irem Altan wrote: Thanks! It solved most of the problem. I am now getting an error during

Re: [gmx-users] Pro-lig under one molecule type

On 2/18/16 12:18 AM, Sana Saeed wrote: hi i am working of protein ligand binding free energy calculation, i have seen some tutorials, like from alchemistry websites and from some paper works. i made ligand topology with acpype (amber.ff) and used pdb2gmx for protein topology, then i combined

Re: [gmx-users] tip4p2005 with gromacs 4.6.5

On 2/17/16 6:29 PM, Irem Altan wrote: Thanks! It solved most of the problem. I am now getting an error during energy minimization: The [molecules] section of your topology specifies more than one block of a [moleculetype] with a [settles] block. Only one such is allowed. If you are trying to

[gmx-users] Triglycerides: Berger Lipids and Kukol Lipids

Hi all, I am currently doing simulations of triglycerides with the Berger parameters. Therefore, I built my topology files based on a phospholipid-file (in my case dppc.itp) from Peter Tielemans homepage (http://wcm.ucalgary.ca/tieleman/downloads). That means, I had to replace all

[gmx-users] Errata corrige: relative binding free energy calculation

Dear users, I’m performing relative binding free energy calculation in Gromacs 5.0.5 of two amino acids: Alanine and Serine (not glycine as I wrongly wrote before). After the minimization phase the simulations crush giving me output file like 'step***.pdb' and the error is 'Fatal error: Too

Re: [gmx-users] Potential energy of protein after energy minimization

Hello Sir I have generated the structure using PHYRE server, performed its structural validations. As per your suggestion I have checked the protein in both visualizing software. During MD simulation of the protein, the pdb2gmx is generating topol.top and .itp without any errors. Do I need to

[gmx-users] Relative binding free energy

Dear users, I’m performing relative binding free energy calculation in Gromacs 5.0.5 of two amino acids: Alanine and Glycine. After the minimization phase the simulations crush giving me output file like 'step***.pdb' and the error is 'Fatal error: Too many LINCS warnings (1000) If you know

Re: [gmx-users] Pro-lig under one molecule type

Thank you Sir for your suggestions. But sir I am simulating only protein in water where pdb2gmx itself generates topol.top and porse.itp files. The topol.top file is already have command to include .itp file generated by gmx. In editconf defining boxtype with cubic and dimension 1.0. On Thu, Feb

Re: [gmx-users] Pro-lig under one molecule type

HI, you can follow this tutorial ,you might seen it but missed the part of topol.top you have to include *itp files and Molecules in topology,it is very easy There are lots of threads in this mailing list regarding this, http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-

[gmx-users] Potential energy of protein after energy minimization

Hii I am simulating protein (PfCDPK5) in water. After performing energy minimization, the potential energy of my protein is 2.86082e+07. As mentioned in the tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html, the Epot should be negative. The