Re: [gmx-users] Question about n-linked glycans

On 9/27/14 11:15 PM, Mikhail Yustanov wrote: Hi all, I am trying to study the influences of N linked glycans on protein stability. I am very new to MD Simulations. I wonder what is the best way to generate a topology file for the glycoprotein. Is there AMBER/GLYCAM integrated force field pr

Re: [gmx-users] Regarding siRNA simulation.

On 9/28/14 7:36 AM, Anurag Dobhal wrote: I am simulating an RNA molecule in which first residue has a 5'-PO4 cap, which is uncommon. I am adding the atoms and bond parameters in the .rtp files in the existing force field directories but these parameters are not getting saved. I am using Amber

Re: [gmx-users] On the ussing of different equilibration protocols in NPT

On 9/28/14 7:41 AM, James Starlight wrote: Thank you very much for the suggestion! How do you think are there any drammatic differences between different preassure coupling (barostats) methods implemented not only in Gromacs but in other md packages like amber and namd? What barostat will be be

Re: [gmx-users] Regarding GROMACS Tutorial "KALP15 in DPPC"

On 9/28/14 9:14 AM, Anurag Dobhal wrote: Hey gromacs users I got the confout.gro file by running the command mdrun -v -deffnm em -o confout.gro and then i ran the command " perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat " but now the teminal says that Read

Re: [gmx-users] Regarding GROMACS Tutorial "KALP15 in DPPC"

On 9/29/14 4:44 AM, Anurag Dobhal wrote: hello justin Can you please tell me how will i solvate my system. which command will i use and what will be my input and output file. Consult a basic tutorial for this information. The membrane protein tutorial assumes the user is already familiar

Re: [gmx-users] AMBER FF naming and caps

On 9/29/14 5:58 AM, Ebert Maximilian wrote: Dear list, I am a little bit confused regarding the preparation needed to use the AMBER FF in GROMACS 5.0.1. I have a simple PDB file of a protein and I use this as input to pdb2gmx. I selected the AMBER FF during the creation process: gmx_mpi pd

Re: [gmx-users] Problem with constraints in NVT calculations.

On 9/29/14 8:01 AM, Kester Wong wrote: Dear all, I have been using the SWM4-NDP water model that works well with CHARMM27 force field. Time out. SWM4-NDP is a polarizable water model, and CHARMM27 is an additive force field. The two are not compatible. If you're using them together, yo

Re: [gmx-users] Regarding Umbrella samplling

On 9/29/14 10:09 AM, Sathish Kumar wrote: Dear gromacs usres, I have run the umbrella sampling with the help of tutorial of justinIn my system rna is binding with gold nanoparticle...to find out the binding energy i run the umbrella sampling using the space 0.2 nm and i got total 59 conf

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

On 9/30/14 5:51 AM, Anurag Dobhal wrote: Hello gromacs users. I am running GROMACS Tutorial of KALP15 in DPPC. I am in the step define box and solvate. after the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat i am getting an error as Use of uni

Re: [gmx-users] minimization for final configuration

On 9/30/14 3:36 AM, Mahboobeh Eslami wrote: hi GMX users i have simulated the protein-ligand complex by gromacs for 20ns. The average for the final structure of 18 to 20 nanoseconds has been achieved.is minimization for the final average structure required?Sincerely. An average structure mi

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

something that you click on to magically open. It's just a listing of coordinates. Visualize it in VMD. Inspect its contents with a text editor. -Justin I again repeated the tutorial and I am getting the same things. Thank you again for your time. On Tue, Sep 30, 2014 at 4:16 PM, Justin L

Re: [gmx-users] potassium ion in GROMOS

On 9/30/14 8:32 AM, h.aliza...@znu.ac.ir wrote: Dear users, How can we define potassium ion in GROMOS ions.itp file? Exactly like the other ions. If there are suitable K parameters, define the [moleculetype] and add the nonbonded parameters for the new atom type in ffnonbonded.itp. -Just

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

On 9/30/14 10:30 AM, Anurag Dobhal wrote: Dear justin Thank you for your rely and precious time. I am aware that .gro file is to be visualized in VMD and its content can be checked in text editor. all the previous .gro file are visualized and checked in VMD. I have obetained that ( confout.g

Re: [gmx-users] Fw: minimization for final configuration

On 9/30/14 9:58 AM, Mahboobeh Eslami wrote: dear Justin thanks for your reply The plot of the RMSD against time for the trajectory generated with g_rms shows a maximum RMSD about 0.195 nm. I set cut-off value to 0.2 nm for g_clusters command. Is it a appropriate value? g_rms and g_cluster do

Re: [gmx-users] watrebox with osmolites

On 9/30/14 3:31 PM, niyaz.sabir wrote: Dear Gromacs users, Is there any tutorial to simulate a protein in water solution containing neutral zwitterionic osmolite such as trimethylglycine? Evaluating effects of the compound on protein stability/secondary structure flexibility is to be conside

Re: [gmx-users] Force field for phosphoserine

On 10/2/14 8:45 AM, ashish bihani wrote: Hello everyone,Has anyone subjected a polypeptide containing a phosphoserine residue to :~$ pdb pdb2gmx ? The program does not recognize serine as it has a phosphorus atom attached to it which is not present in the definition. I am trying to define ph

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

On 10/2/14 8:50 AM, Anurag Dobhal wrote: Thanks Justin I m running the command " mdrun -s em.tpr " and I did get the confout.gro file as output. after that I am running the command " perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat " and then again the ene

Re: [gmx-users] parachem GMX

On 10/2/14 9:21 AM, xy21hb wrote: Dear all, I have used parachem to generate the topology file in .str format. Since I would like to use it in GROMACS software, I wonder how I can convert it to CHARMM force field format in GROMACS. Use our converter: http://mackerell.umaryland.edu/charmm

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

On 10/2/14 12:51 PM, Anurag Dobhal wrote: how will I get to know that the system have shrunken enough, and which file I need to solvate. This is stated in the tutorial. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdocto

Re: [gmx-users] Martini force field - coarse grained protein tutorials

On 10/2/14 1:39 PM, David Ackerman wrote: Hello, I am also attempting to run Martini using version 5 and am getting the same two errors with an mdp file that worked (aside from warnings) on version 4.6.5. Does anyone have a solution to this problem? It's because the default cutoff scheme ha

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

On 10/3/14 6:21 AM, Anurag Dobhal wrote: hello Justin thanks for your reply. I am unable to understand how to proceed in this tutorial. I am working on it from many days but I am unable to do. I have understood till the step. perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area

Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

On 10/3/14 7:48 AM, Anurag Dobhal wrote: How to iteration the system 26 times. I am unable to understand that part. please explain how to do it. Please have a bit of patience when waiting for a reply rather than spamming the list every hour with follow-ups. It took quite a while for me to

Re: [gmx-users] Polymer parameter

On 10/3/14 7:47 AM, Lovika Moudgil wrote: Hi everyone , I have a polymer DEAE-Dextran . I want to generate parameters for it that can be used in gromacs . Please guide me how can I do ? I have already tried generating .itp with ATB and using it ...but it's not working http://www.gromac

Re: [gmx-users] Why should I repeat my simulation?

On 10/4/14 5:15 PM, fatemeh ramezani wrote: Dear gmx-users I performed a MD simulation with gromacs software and after sending my results to a journal, referee said "Simulations needs to be repeated with different initial velocity (seed) to make sure that the results are not simulation artif

Re: [gmx-users] Can Gromacs do this?

On 10/6/14 6:22 PM, 折晓会 wrote: Hello everyone, I am a new Gromacs user, and I want to make sure that if Gromacs can be used to simulate air molecules such as oxygen, hydrogen, nitrogen, water vapor, etc. The reason why I plan to use Gromacs is that I need polarizable water model. From the

Re: [gmx-users] Problem with constraints in NVT calculations.

On 10/6/14 10:35 PM, Kester Wong wrote: Dear Justin and all, 원본 메일 - *보낸사람* : Justin Lemkul *받는사람* : *받은날짜* : 2014년 9월 29일(월) 21:32:13 *제목* : Re: [gmx-users] Problem with constraints in NVT calculations. On 9/29/14 8:01 AM, Kester Wong wrote

Re: [gmx-users] Dead inflategro.pl link?

On 10/7/14 4:17 PM, andrew biedermann wrote: I am working through the second tutorial from Dr. Justin A. Lemkul's tutorial site and have run into a problem finding the inflategro.pl file online. When I try the link in the tutorial I get the error: Firefox can't find the server at www.csb.bit.

Re: [gmx-users] Regarding msd

On 10/8/14 3:21 AM, rajat desikan wrote: Hi, You need to use -pbc nojump to calculate the msd. Using -pbc whole is wrong for calculating the msd. Upon what do you base this statement? I get identical results with an unprocessed trajectory, and those treated with either -pbc whole or -pbc n

Re: [gmx-users] "Warning: For efficient BFGS minimization, use shift/switch/PME instead of cut-off"

On 10/8/14 2:26 AM, GAYATHRI S wrote: Thank you for your suggestions. I followed your instruction and applied potential modifier during energy minimization. However, the problem still persists. Please suggest what to do. OK, so there's simply a problem with input checking in grompp. This

Re: [gmx-users] Problem with constraints in NVT calculations.

On 10/7/14 10:59 PM, Kester Wong wrote: Hi Justin, Thank you for the clarification. I should look into using NAMD. The new polarisable Drude implementation will surely benefit everyone in the MD community. I am looking forward to using it, as with others (I think there was a similar post by

Re: [gmx-users] Changing constraints algorithm.

On 10/8/14 7:24 AM, Dawid das wrote: Dear gromacs experts, Is it allowed to change constraints algorithm (e.g. from LINCS to SHAKE) during MD simulation? Let's say that simulation crashes because LINCS constraints are not satisfied. Can I go from LINCS to shake in the middle of simulation and

Re: [gmx-users] BASIC FOUNDATION/CONCEPTS used in GROMACS

On 10/8/14 7:18 AM, amitabh jayaswal wrote: Dear All, Greetings! 1. By education and training and experience I've been a Biologist. 2. I'm attempting MD Simulations for the first time in life. 3. Because of the neatly designed tutorials by Dr. J. Lemkul I've been able to do MD of/from the tutor

Re: [gmx-users] Problem with constraints in NVT calculations.

On 10/8/14 8:57 AM, Kester Wong wrote: Hi Justin, > Meanwhile, is it possible to implement a self-consistent FF from scratch? One > example I came across is from the work by Ho and Striolo > > titled: Polarizability effects in molecular dynamics simulations of the > graph

Re: [gmx-users] atoms over 100,000

On 10/9/14 11:27 AM, Erik Marklund wrote: Hi, No, start over from 1. Remember that gro-files are fixed format. Erik On 9 Oct 2014, at 16:19, Albert wrote: thx a lot for the reply. But if I would like to define atom 100'001, should I just specify 100'001 directly and Gromacs will treat

Re: [gmx-users] atoms over 100,000

On 10/9/14 11:32 AM, Albert wrote: thanks a lot for clarification. I've got one more question, are the cases the same for plumed.dat file for patched PLUMED MD simulation in Gromacs? Presumably. PLUMED interfaces with Gromacs, so I'd have to assume that fundamental utilities like index gr

Re: [gmx-users] lipid membrane study and the increase in z dimension on dppc128.gro

On 10/10/14 2:02 AM, rama david wrote: Dear Friends, I want to do the simulation of lipid membrane with peptides. Peptide concist 8 amino acid.I want to keep the two or four peptide just away from membrane and want to see how they interact with membrane. I choose the DPPC mem

Re: [gmx-users] v-rescale fatal error

On 10/10/14 7:36 AM, Kester Wong wrote: Hi Mark, I think it was due to the charged groups in my temp. coupling setting; I had the H3O cation(s) and Cl anion(s) grouped separately: tc-grps = GRA SOL H3O Cl- ; Time constant (ps) and reference temperature (K) tau-t

Re: [gmx-users] Problem with constraints in NVT calculations.

On 10/10/14 4:59 AM, Kester Wong wrote: Hi Justin and all, > > Meanwhile, is it possible to implement a self-consistent FF from scratch? One > > example I came across is from the work by Ho and Striolo > > > > titled: Polarizability effects in molecular dynamic

Re: [gmx-users] lipid membrane study and the increase in z dimension on dppc128.gro

On 10/10/14 7:51 AM, rama david wrote: Dear Justin, Thank you a lot for immediate reply. One more question: Should I need to equilibriate the membrane after this one ?? Even Tieleman's pre-equilibrated membranes are only from a few ns of simulation time; I would always equilibrate

Re: [gmx-users] Free Energy Change of Growing a Molecule

On 10/10/14 10:45 AM, Barnett, James W wrote: Good morning, I'm looking at doing a free energy change with thermodynamic integration with GROMACS. Specifically I want to "grow" a molecule and find out the difference in the free energy. For example, I would like to see the free energy change b

Re: [gmx-users] Acetone parameters and transferability question

On 10/10/14 6:16 PM, Ioanna Styliari wrote: Dear gmx users, I am using Gromacs 4.6.5 to simulate some amphiphilic diblock copolymers (for which I have created the .rtp files) in acetone and water mixtures. I am using the GROMOS53a6 force field. At the beginning I used the Automated Topology B

Re: [gmx-users] Acetone parameters and transferability question

On 10/12/14 5:38 AM, Ioanna Styliari wrote: Hello Justin, and thank you for your reply. Yes, the diffusion constant with the ATB acetone (code name _LVN) was overestimated in a variety of molar ratios (used SPC water), but also, I am not able to reproduce acetone's experimental density correct

Re: [gmx-users] Acetone parameters and transferability question

On 10/12/14 2:59 PM, Ioanna Styliari wrote: Thank you both very much for your very useful comments! Just to clarify, when you say "tweak the parameters", would just an investigation of the change of the charges be sufficient? There's no way to know that, but hopefully so. The charges from A

Re: [gmx-users] entangled polymer chain

On 10/13/14 6:27 PM, unipa wrote: hi, i wold know how in this file what does means the element in the III and IV colums? ffoplsaa.rtp: ; Polyethylene - this is an internal residue [ Eth ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140

Re: [gmx-users] Distance Restraints set for water-ion cluster in gas phase (vacuum)

On 10/13/14 4:48 AM, liuyong_1...@dicp.ac.cn wrote: Dear gromacs usres, I want to run nvt simulation of water-ion cluster (Na+(H2O)250) in gas phase (vacuum) at higher temperature ( bigger than 200 K). But the cluster will collapse at high temperature. So the distance restraints is used to r

Re: [gmx-users] Fatal error: Atom O in residue BTC 1 not found in rtp entry with 156 atoms while sorting atoms

On 10/13/14 8:17 AM, Nilesh Dhumal wrote: Hello, I am getting a following error for pdb2gmx. Fatal error: Atom O in residue BTC 1 not found in rtp entry with 156 atoms while sorting atoms Could anyone tell whats going wrong? Atoms named O1 or O2 get translated per xlateat.da

Re: [gmx-users] Regarding umbrella samplling

On 10/13/14 1:08 PM, Sathish Kumar wrote: I am not able to find wheather the windows are overlaped or not. Please help me in this. You've got a gap in the sampling exactly where g_wham tells you. The histograms show this. You either need more windows or a different force constant, or both

Re: [gmx-users] Error on gromacs running: Attempting to read a checkpoint file of version 15 with code of version 12

On 10/13/14 8:50 PM, ookami a wrote: Dear gmx user: I got this error:Attempting to read a checkpoint file of version 15 with code of version 12, when i'm running my simulation for npt process. Anyone know how could i fix this and why does this happen? I'm running my simulations at Gromacs 4.5.5

Re: [gmx-users] grompp Segmentation fault

On 10/13/14 10:42 PM, Nilesh Dhumal wrote: hello, I running grompp for simulation. I get Segmentation fault error. grompp -f 600.mdp -c cu.gro -p cu_btc_1.top -o 1.tpr checking input for internal consistency... processing topology... Segmentation fault Could any one tell what is the prob

Re: [gmx-users] regarding confout.gro

On 10/14/14 12:31 AM, RINU KHATTRI wrote: hello gromacs user i am working on protein ligand complex with popc membrane i am running production md in extended time (40 ns) i got some file i am using -noappend option i got confout.gro file in each extended time what is the use of this file if i w

Re: [gmx-users] Problem with constraints in NVT calculations.

On 10/14/14 7:40 AM, Kester Wong wrote: Hi Justin and all, > > > > Meanwhile, is it possible to implement a self-consistent FF from scratch? One > > > example I came across is from the work by Ho and Striolo > > > > > > titled: Polarizabili

Re: [gmx-users] How long run should be enough for Free Energy Calculation of a protein?

On 10/14/14 11:37 PM, Batdorj Batsaikhan wrote: Dear gmx-users, Hello, I am working on free energy calculation of a protein. How long run should be enough for Free Energy Calculation of a protein? How is it that you're attempting to calculate this quantity? -Justin -- ===

Re: [gmx-users] Unstable system [was: (no subject)]

Please remember to use a sensible subject line. On 10/15/14 6:53 AM, Padmani Sandhu wrote: Hello I have energy minimized the complex successfully and I dont understand whats wrong with the system. What were Epot and Fmax from minimization? Please copy and paste the actual output. What f

Re: [gmx-users] regarding confout.gro

On 10/15/14 6:25 AM, RINU KHATTRI wrote: hello justin i have been visualized the file of confout.gro file in vmd and the position of protein and ligand is ok i know i have to analyze all the parameters like energy and rmsd is it sufficient to extend my simulation or which file i have to visuali

Re: [gmx-users] retaining the active site water molecules in the protein -reg

On 10/15/14 5:06 AM, venkatesh s wrote: hello In my task some water molecules in one protein active site and it playing one of the role of interactions and binding affinity if i want retain that water molecules in active site to preform the simulations what i want to do ? further Simply ret

Re: [gmx-users] Velocity Verlet integrator

On 10/15/14 7:30 AM, Mario Fernández Pendás wrote: Dear all, I am still interested in some integrator related issues. I understand that the easiest way to implement velocity Verlet was to split the updates in two updates. But I don't understad the order of those updates. I mean why there are

Re: [gmx-users] How to add iron parameter?

On 10/15/14 2:05 PM, Johnny Lu wrote: Pure md doesn't deal with complex orbitals well, I guess. Hydrogen bonds in pure md is not directional, as it should be. can molecular dynamics (md) simulate heavy metals, like iron, which have d oribtals? I heard that even calcium is a bit troublesome in

Re: [gmx-users] Unstable system [was: (no subject)]

On 10/15/14 12:35 PM, Padmani Sandhu wrote: Hello Justin, Epot = -3.4264112e+07 Fmax= 8.5767386e+02 from energy minimization. Seems reasonable. I am using force field Gromos43a1 and ligand parameters were derived from PRODRG. PRODRG produces topologies full of errors. Have you done a

Re: [gmx-users] g_dist as an alternative for g_saltbr

ehave. My question is concerning the situation where you still don't know which are the salt bridges in the system and, after that, which are the ones you should take a closer look (I think the obvious approach would be to search literature, but that is not always successful). Justin Lemkul has

Re: [gmx-users] how to build topology

On 10/15/14 4:40 PM, Victor Rosas Garcia wrote: darn it! I was hoping the answer would be different. :( Perhaps I can take the topology from acpype and tweak the atomtypes by hand. Are there any caveats or potential traps in doing this? The authors provide the entire Gromacs-compatible for

Re: [gmx-users] how to build topology

On 10/15/14 5:11 PM, Victor Rosas Garcia wrote: but... the lipids I am interested in are not included in the files provided by the authors. I want to make a new lipid that is compatible with said forcefield. I see no advantage in trying to use acpype or any other tool, just to change the en

Re: [gmx-users] Unstable system [was: (no subject)]

at 1:50 AM, Justin Lemkul wrote: [image: Boxbe] <https://www.boxbe.com/overview> This message is eligible for Automatic Cleanup! (jalem...@vt.edu) Add cleanup rule <https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3Dcn7kjseE1qsZ3%

Re: [gmx-users] How long run should be enough for Free Energy Calculation of a protein?

On 10/16/14 2:51 AM, Batdorj Batsaikhan wrote: I want to calculate free energy of 2 different types of 71 amino acids long protein. I run General Equilibration (NPT). Then I run free energy calculation of 200 ps. When calculation start, I got following warming message: ***

Re: [gmx-users] free energy calculation

On 10/16/14 5:02 AM, elham tazikeh wrote: Dear users For calculating free energy of methan (in justin tutorial) I changed important parameters instead of the parameters in lambda=0 that having in that tutorial Is it correct? If you're trying to execute the tutorial, no, don't make any chang

Re: [gmx-users] How to calculate protein-surface interaction energy

On 10/16/14 5:46 AM, James Lord wrote: Dear users, I want to calculate the interaction energy (energy versus time) of a protein (Lysozyme) adsorption process (20ns) on to a solid surface (polyethylene). when I use gmx energy -f md.edr -o energy.xvg and then selecting total energy I end up with

Re: [gmx-users] The flat-bottomed position restrain in the topolgy file

On 10/16/14 8:12 AM, liuyong_1...@dicp.ac.cn wrote: Dear gromacs usres, The format of the flat-bottomed position restrain in the topolgy file is [position_restraints] ; num. atomsfunc.type g r(nm)k(KJ*mol-1*nm-2) 1 21 1.0 1.0 as given in t

Re: [gmx-users] TWO AMINOACIDS WITH SAME NUMBER IN .GRO FILE

On 10/16/14 8:13 AM, Michetti Davide wrote: Dear gmx users, I have just realized, at the end of a molecular dynamics simulation, that I had in my .gro file to aminoacids with the same number. This happened cause in my pdb file, what was supposed to be residue 53, was instead 52A (due to an i

Re: [gmx-users] free energy calculation for methane

On 10/16/14 9:33 AM, elham tazikeh wrote: Dear Justin thanks for your reply i trying to follow your tutorial but when i want to produce neccesary files per lambdas by this command: Perl write_mdp.pl em_steep.mdp i received 20 files as i expected but they are empty, No idea. Works perfectly

Re: [gmx-users] error in free energy calculation

On 10/16/14 9:57 AM, elham tazikeh wrote: Dear Justin when I am doing this tutorial *sh mklambdas.sh run.mdp topol.top equil.gro* I got following error: *mklambdas.sh: 12: mklambdas.sh: Syntax error: "(" unexpected* How can I fix this? Well, apparently there's a syntax error in the scr

Re: [gmx-users] How to calculate protein-surface interaction energy

On 10/16/14 10:47 AM, James Lord wrote: Hi Justin, Thanks, the .mdp is the same as your tutorial for lysozyme, Can you explain a bit more what to do? if I want to have total energy= vdw and electrostatic? energygrps = Protein Surface or whatever the names should be. -Justin --

Re: [gmx-users] How to calculate protein-surface interaction energy

On 10/16/14 11:42 AM, James Lord wrote: Hi Justin, Sorry for not being clear, I have done the simulation without specifying the energygrps, so based on your previous comment I should use mdrun -rerun trj.xtc -o energy.edr -pn index.ndx? and in index file define energygrps = Protein Surface rig

Re: [gmx-users] Parameter conversion from GAFF to Gromacs

On 10/16/14 1:24 PM, Rohit Farmer wrote: Hi All, I have recently converted the whole of GAFF parameters database to Gromacs format to use with the AMBER 99SB ILDN forcefield. My intention was to simulate a number of ligands which I covalently bound to a residue in the protein. So if I bind som

Re: [gmx-users] pdb2gmx ffG43a1 force field

On 10/16/14 10:55 PM, Nilesh Dhumal wrote: Hello, I am generating .top file using pdb2gmx and choose ffG43a1 force field from the list. pdb2gmx is running for an hour. Here I pasted the last part appeared on screen Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 for

Re: [gmx-users] fatal error in gromacs

On 10/17/14 6:36 AM, Yaser Hosseini wrote: hi gromacs users when i want to run pdb2gmx command i got a fatal error that said : the residue from MN has lost. and i used all of force feild but i got this error how can i fix it and which one of force feild coomand can i use?? Mn is probably

Re: [gmx-users] pressure dependence on volume.

On 10/17/14 11:49 AM, Johnny Lu wrote: At least for real water, a 0.2% error in volume can mean the pressure is ~30 bar when the target pressure is 1 bar. http://docs.engineeringtoolbox.com/documents/309/water-density-temperature-pressure_2.png On Fri, Oct 17, 2014 at 10:49 AM, Johnny Lu wrot

Re: [gmx-users] g_dist as an alternative for g _saltbr

On 10/17/14 2:13 PM, Diogo Martins de Sá wrote: Dear Justin, thanks for your reply. To start with, here are the links where you mentioned "looping calculations" (http://article.gmane.org/gmane.science.biology.gromacs.user/59569/match=g_saltbr+looping+calculations) and "track persistence of int

Re: [gmx-users] pdb2gmx ffG43a1 force field

On 10/17/14 4:09 PM, Nilesh Dhumal wrote: Hello, I am generating .top file using pdb2gmx and choose ffG43a1 force field from the list. pdb2gmx is running for an hour. Here I pasted the last part appeared on screen Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 forc

Re: [gmx-users] g_dist as an alternative for g _saltbr

On 10/17/14 4:49 PM, Diogo Martins de Sá wrote: That can certainly work for me! Especially because I know my groups "functional groups". I guess if one was still in doubt what to focus on, then my idea could still be useful (with a bit more of work). Now, just so I get things right: 1. I got

Re: [gmx-users] pdb2gmx ffG43a1 force field

On 10/17/14 4:53 PM, Nilesh Dhumal wrote: All are from same residue. I added following part in .rtp file. [ BTC ] [ atoms ] Cu Cu 1.0980 OA O -0.665 0 OB O -0.665 0 CA C 0.778 0 CB C -0.092 0 CC C -

Re: [gmx-users] Understanding comments in pdb2gmx output

On 10/17/14 6:08 PM, Agnivo Gosai wrote: Dear Gromacs Users I am working with a complex of Human Thrombin - DNA aptamer ( pdb id 1HAO ) . I am using GROMACS 4.5.7 having the force field AMBER99SB-ParmBSC0 ported into it. I had cleaned the PDB file off crystal waters and a small chemical ligand

Re: [gmx-users] lipid membrane study and the increase in z dimension on dppc128.gro

On 10/18/14 2:26 AM, rama david wrote: Dear Justin, I added the water as per your instruction and following the instruction from http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations I change the box size by editconf and vdwradii.dat files carbon radii to 0.45. I adde

Re: [gmx-users] free energy for ethanol

On 10/18/14 1:38 AM, elham tazikeh wrote: Dear Justin i really appriciate for your reply i trying to follow this tuturial about free energy of ethanol: *http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf * there was

Re: [gmx-users] How to calculate protein-surface interaction energy

On 10/18/14 6:45 AM, James Lord wrote: Dear Justin & Diogo, Thanks for your comments, I did the steps you guys mentioned to calculate protein-suface interaction energy and expect to see "protein surface" option upon running g_energy but it is not the case, any comments? Here is what I did, gedi

Re: [gmx-users] How to calculate protein-surface interaction energy

On 10/18/14 8:51 AM, James Lord wrote: Hi Justin, Thanks for the prompt answer. I selected LJ-(SR) but I am getting a positive fluctuating line over the simulation time. Looking at the vmd movie I can see that protein (Lysozyme) is coming into contact with surface afte 10ns and is 5 nm away at

Re: [gmx-users] How to calculate protein-surface interaction energy

On 10/18/14 9:30 AM, James Lord wrote: Hi Justin, 1. Make sure your index groups are correctly constructed. Do I need to use make ndx? I thought just adding energygrps=protein surface at the end of .mdp is enough? "Surface" isn't likely a default group (unless that's the name of the [molec

Re: [gmx-users] How to calculate protein-surface interaction energy

your files, it's impossible to diagnose that any further. -Justin rvdw=1 nm so should be fine. and for the last part I agree. Cheers James On Sun, Oct 19, 2014 at 2:34 AM, Justin Lemkul wrote: On 10/18/14 9:30 AM, James Lord wrote: Hi Justin, 1. Make sure your index groups are

Re: [gmx-users] Understanding comments in pdb2gmx output

On 10/18/14 3:59 PM, Agnivo Gosai wrote: Dear Users Thrombin-Aptamer complex : PDB ID 1HAO Thanks for the earlier comments. I appreciate the efforts of all users and developers for taking their time out and helping. I checked the pdb file for the "occupancies" not equal to 1.000 and found 9

Re: [gmx-users] boron atom parameter

On 10/18/14 3:39 PM, fatemeh ramezani wrote: Dear gmx users I am performing a simulation by gromacs. My ligand molecule has a boron atom and by topology builder softwares such as prodrg, ATB, swiss param, antechamber I get an error that boron atom is not supported by this program. Do you hav

Re: [gmx-users] boron atom parameter

Please keep the discussion on the gmx-users mailing list. On 10/18/14 5:00 PM, fatemeh ramezani wrote: Dear Dr. Justin I have boron parameter from a paper. Can I prepare top file by the below method? I replace boron atom with carbon in my ligand structure and I get a top file from prodrg, the

Re: [gmx-users] How to calculate protein-surface interaction energy

On 10/18/14 8:41 PM, James Lord wrote: Hi Justin, Thanks, apparently I am doing some silly mistakes as I checked for another system I have and ended up to the same problem. I am sending all the files to your personal email and then if the problem is solved I will send a post with description of

Re: [gmx-users] How to calculate protein-surface interaction energy

On 10/18/14 10:41 PM, James Lord wrote: Hi Justin, Here is the uploaded files on 4share. http://www.4shared.com/folder/9CgRBgqp/_online.html Well, I tried clicking three different things that said download, but every one of them tried to download software, spam, or charge me money, so I'm go

Re: [gmx-users] free energy problem

On 10/19/14 5:14 AM, elham tazikeh wrote: Dear Justin thanks for your replys and your patient i think my main problem is the way of using of perl/shell scripts in your tutorial (Free energy for methane) my question is: for script using, i must be execute them by *(chmod +x ...) * and then us

Re: [gmx-users] How to calculate protein-surface interaction energy

On 10/19/14 7:26 AM, James Lord wrote: Hi Justin, Well, I tried clicking three different things that said download, but every one of them tried to download software, spam, or charge me money, so I'm going to assume that the files you sent me off-list are the same ones you've posted here. If th

Re: [gmx-users] how to treat the peptide apart from the ligand -reg

On 10/19/14 12:36 PM, venkatesh s wrote: i generated peptide .gro .file and top using *prodrg *server so here after how to update the topol.top ? (Distance restrain or potions restrain ? ) You shouldn't use PRODRG for peptide ligands; the parameters are totally inconsistent with the paren

Re: [gmx-users] OPLSAA

On 10/19/14 1:43 PM, Eric Smoll wrote: Hello Gromacs users, Here is a quote from a JPCB paper with over 500 citations: "In fact, in the specification of the OPLS-AA force field, sites within the same molecule separated by *more than* three bonds interact by Lennard-Jones and electrostatic pot

Re: [gmx-users] free energy question

On 10/19/14 11:31 PM, elham tazikeh wrote: Dear Justin Your mean is, i should use: perl write_mdp.pl em_steep.mdp For creating *.mdp files for EM process per lambdas And for producing for example nvt.mdp,i must write: perl write_mdp.pl nvt.mdp ? Yes, which is exactly what is stated on htt

Re: [gmx-users] free energy calculation

On 10/20/14 6:16 AM, RINU KHATTRI wrote: hello gromacs users i am working on protein complex with popc membrane i want to calculate the free energy of complex i have run protein complex and dppc tutorial how to start for that i am using 4.5 version of gromacs should i use GROMACS Tutorial F

Re: [gmx-users] How to calculate protein-surface interaction energy

On 10/20/14 8:11 AM, James Lord wrote: Hi Justin, Would you please tell me from the files I sent you which of them you checked and how you got to the conclusion that (I mean which command ) "This system behaves correctly - there is a zero interaction energy (both Coulomb and LJ) at t=0, so it

Re: [gmx-users] help

On 10/20/14 9:23 AM, 玻耳兹曼 wrote: dear all I am new in gromacs .I got an error while running the tutorial of KALP15 in DPPC . I issue a command ; grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr , and i received a fatal error : Back Off! Generated 837 of the 2346 no

Re: [gmx-users] Fatal error:No molecules were defined in the system

On 10/20/14 11:19 AM, Nilesh Dhumal wrote: Hello, For grompp grompp -f minim_hy.mdp -c cu.gro -p test.top -o 1.tpr I get the error" Fatal error:No molecules were defined in the system" Here I pasted initial part of test.top file. ; Derived from parsing of runfiles/alat.top.orig [ defaul

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