Re: [gmx-users] (no subject)

Start here: http://www.mdtutorials.com/gmx/. An introduction to linux book might be helpful as well if you are not already familiar with it. Good luck! On Thu, Apr 2, 2020 at 2:05 PM Feriel Terbeche wrote: > Hello! > My name's FERIEL TERBECHE I am a genetic studant, from ALGERIA, Im >

Re: [gmx-users] (no subject)

Download and use the forcefield files from the ATB server website, and then make that you correctly point to it in your top file. On Sat, 14 Mar. 2020, 7:32 pm FAISAL NABI, wrote: > Hi, > I have been a new user and i was following the protein-ligand complex > tutorial for MD. I have used

Re: [gmx-users] no subject

Hello Faisal, Easiest way to do this is by navigating to the MD files tab and download the "Gromacs 4.5.x-5.x.x 54a7" below this warning - "*Warning!* This molecule contains non-standard atom types not included in the standard GROMOS 54A7 forcefield..." The folder contains the procedure to

Re: [gmx-users] (no subject)

Thanks christian for the detailed description. On Mon, Feb 17, 2020 at 8:00 PM Christian Blau wrote: > Hi Shakkira, > > > The simulation box deformation is described by six parameters that > describe three basis box vectors with the following > contraints, > > - the first box vector is

Re: [gmx-users] (no subject)

Hi Shakkira, The simulation box deformation is described by six parameters that describe three basis box vectors with the following contraints,  - the first box vector is aligned along the x-axis, with coordinates thus has coordinates (xx,0,0)  - the second box vector is aligned in the x-y

Re: [gmx-users] (no subject)

On 2/14/20 12:05 AM, Neha Tiwari wrote: Dear Gromacs experts, I have generated topology files(.itp) of the ligand from the ATB server and everything goes well, but when it comes to generating ions.tpr file, I am getting following error. $ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o

Re: [gmx-users] (no subject)

for what reasons you request the largest force in your system smaller than such small value? On Fri, Jan 24, 2020 at 1:22 PM Sadaf Rani wrote: > Dear Gromacs users > I am running a free energy calculation of the protein-ligand complex. > During the energy minimization process, I am getting many

Re: [gmx-users] (no subject)

On 12/25/19 11:14 PM, Najamuddin Memon wrote: It is not about to select numbers in drop down menu. You should write atom no of protein and ligand. For example your chain a is protein having 2000 atoms. The atom no starts from 1 till 2000 for protein. And for chain b is your ligand and your

Re: [gmx-users] (no subject)

It is not about to select numbers in drop down menu. You should write atom no of protein and ligand. For example your chain a is protein having 2000 atoms. The atom no starts from 1 till 2000 for protein. And for chain b is your ligand and your ligand has 40 atoms it is from 2001 till 2040. You

Re: [gmx-users] (no subject)

Ok i will try, thank you so much On Mon, 9 Dec 2019, 1:07 pm Tasneem Kausar, wrote: > This problem also occurs in gromacs-5.1.4. Try higher version. We have done > these calculations on gromacs-2016. > > On Mon, Dec 9, 2019 at 10:49 AM shakuntala dhurua < > madhu.dhuru...@gmail.com> > wrote: >

Re: [gmx-users] (no subject)

here I am using gromacs version --- gromacs-5.1.5 On Mon, Dec 9, 2019 at 10:43 AM Tasneem Kausar wrote: > Please specify your gromacs version. > > On Mon, Dec 9, 2019 at 10:04 AM shakuntala dhurua < > madhu.dhuru...@gmail.com> > wrote: > > > hi > > I am facing problem during hydrogen bond

Re: [gmx-users] (no subject)

Please specify your gromacs version. On Mon, Dec 9, 2019 at 10:04 AM shakuntala dhurua wrote: > hi > I am facing problem during hydrogen bond correlation c(t) with error > segmentation fault > I have used following flag for generate xtc file::- gmx trjconv -n > index.ndx -s ins_prod_1.tpr -f

Re: [gmx-users] (no subject)

On 11/19/19 5:55 AM, Bratin Kumar Das wrote: Hi I hope there is a problem in the topology...please follow the gromacs tutorial.. More specifically: http://www.mdtutorials.com/gmx/complex/index.html The #include statements are out of order. You cannot add new parameters to the

Re: [gmx-users] (no subject)

Hi I hope there is a problem in the topology...please follow the gromacs tutorial.. On Tue 19 Nov, 2019, 3:34 PM Alessandra Villa, < alessandra.villa.bio...@gmail.com> wrote: > Hi, > Pls note that the maillist does not support attachments. > Also it will better/helpful to use emails subject.

Re: [gmx-users] (no subject)

Hi, Pls note that the maillist does not support attachments. Also it will better/helpful to use emails subject. Kind regards Alessandra On Tue, Nov 19, 2019 at 10:46 AM pooja kesari wrote: > Dear All, > I am doing a protein-ligand simulation, when i was try to *add ions to the > system* > gmx

Re: [gmx-users] (no subject)

thanks Prof. Justin On Tue, Nov 12, 2019 at 8:48 PM Justin Lemkul wrote: > > Please use an appropriate subject line. > > On 11/12/19 5:29 AM, shakuntala dhurua wrote: > > hello, > > Here I want to generate arg.pdb to arg.gro by using amber99sb force > field . > > for test i have used 1 residue

Re: [gmx-users] (no subject)

thanks Bratin for your suggestion On Tue, 12 Nov 2019, 7:54 pm Bratin Kumar Das, <177cy500.bra...@nitk.edu.in> wrote: > I think you have capped your residue in the N-terminal and C-terminal > end...and the capping is not defined in your .rtp entry.. that's why this > error is coming > > On Tue

Re: [gmx-users] (no subject)

Please use an appropriate subject line. On 11/12/19 5:29 AM, shakuntala dhurua wrote: hello, Here I want to generate arg.pdb to arg.gro by using amber99sb force field . for test i have used 1 residue of arginine but i got Fatal error: There is a dangling bond at at least one of the terminal

Re: [gmx-users] (no subject)

I think you have capped your residue in the N-terminal and C-terminal end...and the capping is not defined in your .rtp entry.. that's why this error is coming On Tue 12 Nov, 2019, 3:58 PM shakuntala dhurua, wrote: > hello, > Here I want to generate arg.pdb to arg.gro by using amber99sb force

Re: [gmx-users] (no subject)

Thank you sir for your suggestions On Fri, 8 Nov 2019, 7:31 pm Christian Blau, wrote: > Hello Shakuntala, > > > If you already have the trajectories, you have to post-process at least > once to filter the data down to a manageable > size, and once to do the periodic boundary condition fix

Re: [gmx-users] (no subject)

Hello Shakuntala, If you already have the trajectories, you have to post-process at least once to filter the data down to a manageable size, and once to do the periodic boundary condition fix precisely as you described. If you set up a new simulation you may use "nstxout-compressed" to

Re: [gmx-users] (no subject)

Hello Saranya, Now again with readable formatting. Also note that it is very useful to people on gmx-useres to specify the subject when writing emails, because it makes it easier to search, reply, and handle multiple discussion threads. This error means that during the nvt equilibrium high

Re: [gmx-users] (no subject)

Hello Saranya,This error means that during the nvt equilibrium high forces occurred that made it impossible to resolve the bond constraints. The very high forces occurred most likely are due to some high tension in the system. As indicated in the error message you can. Reduce the time step of

Re: [gmx-users] (no subject)

Look in, or search the archive, the responses are there. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/ On Mon, 30 Sep. 2019, 1:02 am Mahsa Rezaei, wrote: > Dear gromacs users, > > Sorry for repeating my question. > > I didn't receive any email so I couldn't reply and I missed >

Re: [gmx-users] (no subject)

I have seen this in Gromacs manual. [ virtual_sites2 ] ; Site fromfunct a 5 1 2 1 0.7439756 for type 3 like this: [ virtual_sites3 ] ; Site from funct a b 5

Re: [gmx-users] (no subject)

On 8/26/19 2:33 PM, Navneet Kumar Singh wrote: I can't understand meaning of this "For all other GROMACS versions, you will have to manually edit the topology to use "3fad" construction and appropriate atom numbers." If I am using version other than the Gromacs2016.x. Can I get example of

Re: [gmx-users] (no subject)

I can't understand meaning of this "For all other GROMACS versions, you will have to manually edit the topology to use "3fad" construction and appropriate atom numbers." If I am using version other than the Gromacs2016.x. Can I get example of any topology file where these kind of construction've

Re: [gmx-users] (no subject)

On 8/26/19 1:14 PM, Navneet Kumar Singh wrote: Do I have to add vsite3 information from unk.itp to system.top files? That directive belongs in the topology to which it corresponds. If it is in unk.itp, then it is already in system.top. You don't need to include anything else. -Justin

Re: [gmx-users] (no subject)

Do I have to add vsite3 information from unk.itp to system.top files? -maxwarn 1 flag I checked in gromacs 16 version and it's running there. On Mon, 26 Aug 2019, 00:58 Justin Lemkul, wrote: > > > On 8/25/19 2:17 PM, Navneet Kumar Singh wrote: > > Yeah! I have read that. > > > > uses -maxwarn

Re: [gmx-users] (no subject)

On 8/25/19 2:17 PM, Navneet Kumar Singh wrote: Yeah! I have read that. uses -maxwarn 1 to produce .tpr file using grompp command as mentioned in Since you are getting an error rather than a warning, that means you are not using GROMACS 2016.x, as the instructions I pointed to you say.

Re: [gmx-users] (no subject)

Yeah! I have read that. uses -maxwarn 1 to produce .tpr file using grompp command as mentioned in python script cgenff_charmm2gmx_py2.py output of cgenff_charmm2gmx_py2.py

Re: [gmx-users] (no subject)

On 8/25/19 11:49 AM, Navneet Kumar Singh wrote: Thank You Sir! Attached file can be downloaded from following link. https://fil.email/OR7Nsh0f Error ERROR 1 [file unk.itp, line 497]:

Re: [gmx-users] (no subject)

Thank You Sir! Attached file can be downloaded from following link. https://fil.email/OR7Nsh0f Error ERROR 1 [file unk.itp, line 497]: Duplicate atom index (23) in virtual_sites3

Re: [gmx-users] (no subject)

On 8/25/19 8:33 AM, Navneet Kumar Singh wrote: can you please help in solving this error while running MD simulation of protein-ligand complex using CHARMM36 force field on GROMACS engine. *Command* *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr* *ERROR* *ERROR 1 [file

Re: [gmx-users] (no subject)

On 8/19/19 2:00 AM, Priyanka Singh wrote: Hii I am new to simulations. I want to ask is it ok to use ligand topology build using PRODRG server if using amber force field for RNA-ligand simulation. what precautions one should take ends of the RNA molecule. PRODRG is for GROMOS and produces

Re: [gmx-users] (no subject)

I think the answer is not so straightforward. It depends upon a lot of things, but I would say that the parameters derived using QM is better. If you do not have any other options you can still use PRODRG server but even in that case, I find many people using the docked (or bound) conformation of

Re: [gmx-users] (no subject) (Soham Sarkar)

Hello, The "?" You are talking about is mistakenly written there. The original itp file has nothing there and is showing the error. The first few lines are commented out. So why is that problem? Sorry for not giving a title. If you want, I can share the original itp file here but as per the

Re: [gmx-users] (no subject)

In molecular dynamics things move around. The fact that the molecules aren't in the starting position shows that it isn't a stable configuration, the interactions between the protein and the molecules are insufficient to keep them together in that spot. Catch ya, Dr. Dallas Warren Drug

Re: [gmx-users] (no subject)

http://manual.gromacs.org/documentation/current/reference-manual/topologies/force-field-organization.html FFs are located in the share/gromacs/top directory. If you have your own FF that isn't included in the distribution with GROMACS, you can either add it to that directory, or have the FF

Re: [gmx-users] (no subject)

Sir, Can anyone suggest how I can use ethanol force field to solvate and run MD for my molecule. Please help. On Thu 31 Jan, 2019, 10:48 AM Satya Ranjan Sahoo Sir, > I am a beginner to GROMACS. I was unable to understand how to create all > the ions.mdp , md.mdp , mout.mdp , minim.mdp ,

Re: [gmx-users] (no subject)

Run the tutorials -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Satya Ranjan Sahoo Sent: Wednesday, January 30, 2019 11:19 PM To: gmx-us...@gromacs.org Subject: [gmx-users] (no subject) Sir, I am a beginner to GROMACS. I was unable to understand

Re: [gmx-users] (no subject)

Hi, There is a detailed online tutorial. http://www.mdtutorials.com/gmx/ It has everything you need. Best, Saumyak On Thu, 31 Jan 2019 at 10:51, Satya Ranjan Sahoo wrote: > Sir, > I am a beginner to GROMACS. I was unable to understand how to create all > the ions.mdp , md.mdp , mout.mdp ,

Re: [gmx-users] (no subject)

Hi, This is one of the examples in the documentation of gmx select. Try looking there! Mark On Fri., 25 Jan. 2019, 07:30 Soham Sarkar, wrote: > Hello Everyone, >I want to calculate some properties of the solvent molecules within > 6angstrom from the protein backbone, for that I need a

Re: [gmx-users] (no subject)

On 12/1/18 8:11 AM, Soham Sarkar wrote: Dear all, This is the error I get while executing the grompp command " Program grompp, VERSION 4.5.6 Source code file: topio.c, line: 582 Fatal error: Syntax error - File tris.itp, line 19 Last line read: ' #error CORRECT VERSION OF FORCE FIELD

Re: [gmx-users] (no subject)

On 11/23/18 12:58 AM, maya nair wrote: I am trying to do the molecular dynamics of DNA-ligand complex. I made the ligand files using antechamber and converted the amber files to .gro and .top using acpype.pl. Then I made the complex.gro. when I am trying to run grommp ions.mdp and em.mdp,

Re: [gmx-users] (no subject)

On 9/23/18 12:11 PM, AKANXA TIWARI wrote: Hi During simulation of protein after giving grompp ions command i got a note what should i do. NOTE 3 [file ions2.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics.

Re: [gmx-users] (no subject)

In your .mdp file ...in cut-off you mention PME... On Sun, Sep 23, 2018, 9:42 PM AKANXA TIWARI wrote: > Hi > During simulation of protein after giving grompp ions command i got a note > what should i do. > NOTE 3 [file ions2.mdp]: > You are using a plain Coulomb cut-off, which might produce

Re: [gmx-users] (no subject)

I suggest this tool:https://github.com/llazzaro/acpype On Friday, September 14, 2018, 10:44:56 PM GMT+3, SAKO MIRZAIE wrote: Hi every one, I need the topology parameters for pyridoxal phosphate linked to lysine with amber99sb force field. does anyone have the mentioned parameters? I

Re: [gmx-users] (no subject)

thanks for reply On Fri, Sep 14, 2018 at 5:09 PM Justin Lemkul wrote: > > > On 9/14/18 6:48 AM, AKANXA TIWARI wrote: > > i am getting a warning after converting pdb2gmx and then applying force > > field what i will do. please help me.i get this on screen. > > WARNING: WARNING: Residue 1 named

Re: [gmx-users] (no subject)

On 9/14/18 6:48 AM, AKANXA TIWARI wrote: i am getting a warning after converting pdb2gmx and then applying force field what i will do. please help me.i get this on screen. WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database,

Re: [gmx-users] (no subject)

You need to add the particular H to the amino acid .rtp file in the forcefield folder On Fri, Sep 14, 2018, 4:24 PM AKANXA TIWARI wrote: > i am getting a warning after converting pdb2gmx and then applying force > field what i will do. please help me.i get this on screen. > WARNING: WARNING:

Re: [gmx-users] (no subject)

On 9/10/18 9:14 AM, Bratin Kumar Das wrote: Use -maxwarn 2 at the last of your gmx grompp ... command No! One should *never* use -maxwarn just to circumvent problems. It is clear that there is some modification to ffnonbonded.itp that is syntactically incorrect. grompp will not have the

Re: [gmx-users] (no subject)

Use -maxwarn 2 at the last of your gmx grompp ... command On Mon, Sep 10, 2018, 6:19 PM saranya wrote: > Dear Users, > > My simulation system is Amyloid β Protein (1-42) with Fe2+ complex > and i am using OPLSAA forcefield for the simulations. I edited the > ffbonded.itp files

Re: [gmx-users] (no subject)

Dear Mark, I think things are not under solution. Please tell me if there is dsDNA of chain A (12 bp) and complimentary strand B(12 bp) like chain A- 3' - 5' chain B- 5' - 3' I am pulling 5' end of strand A and made 5' of B as a reference group along the helical direction under

Re: [gmx-users] (no subject)

Hi Mark Did you get the point or not . Hoping your response On Fri, Aug 31, 2018 at 6:17 PM, Rakesh Mishra wrote: > > *Please remember (its your query to me )* > Hi, > > Can you please share a link to something that indicates why this would be a > good tool for modeling such experimental

Re: [gmx-users] (no subject)

*Please remember (its your query to me )* Hi, Can you please share a link to something that indicates why this would be a good tool for modeling such experimental pulling scenarios? Making the case for implementing such a feature would benefit from that. Mark >

Re: [gmx-users] (no subject)

Dear mark I had already discussed regarding force/extension protocol. But I didn't get any response from your side. I dont have idea to upload some pictures. On Fri, Aug 31, 2018 at 4:05 PM, Mark Abraham wrote: > Hi, > > The list cannot accept attachments. Upload to a file sharing service and

Re: [gmx-users] (no subject)

Hi, The list cannot accept attachments. Upload to a file sharing service and share a link. We will likely need more background information also. Mark On Fri, Aug 31, 2018, 12:22 Rakesh Mishra wrote: > Hi every body > can any one explain what is the mean of this graph > obtained from gromacs

Re: [gmx-users] (no subject)

No I didn't try it. Its a nice idea.. I will try it. On Sun, Jul 22, 2018 at 3:28 AM wrote: > Have you tried the "insert-chemicals-after-md" command ? > > PB > > > On Jul 11, 2018, at 4:50 AM, Mark Abraham > wrote: > > > > Hi, > > > > Are you trying to observe something about the transition,

Re: [gmx-users] (no subject)

Have you tried the "insert-chemicals-after-md" command ? PB > On Jul 11, 2018, at 4:50 AM, Mark Abraham wrote: > > Hi, > > Are you trying to observe something about the transition, or merely the > different end points? > > Mark > >> On Tue, Jul 10, 2018 at 4:12 PM Soham Sarkar wrote: >>

Re: [gmx-users] (no subject)

Thanks a lot.. On Sat, 21 Jul 2018, 9:57 pm Mark Abraham, wrote: > Hi, > > If you want to see whether a helix forms in a given solution, start from a > random coil in that solution. Don't start from a helix in another solution. > > Marm > > On Sat, Jul 21, 2018, 17:41 Soham Sarkar wrote: > > >

Re: [gmx-users] (no subject)

Hi, If you want to see whether a helix forms in a given solution, start from a random coil in that solution. Don't start from a helix in another solution. Marm On Sat, Jul 21, 2018, 17:41 Soham Sarkar wrote: > Dear Mark, > I cant properly get your reply.. If you could elaborate it, it would

Re: [gmx-users] (no subject)

Dear Mark, I cant properly get your reply.. If you could elaborate it, it would be nice - Soham On Sat, 21 Jul 2018, 8:47 pm Mark Abraham, wrote: > Hi, > > Then all you need is the starting point for potential helix formation. You > don't need to see it unravel. > > Mark > > On Sat, Jul 21,

Re: [gmx-users] (no subject)

Hi, Then all you need is the starting point for potential helix formation. You don't need to see it unravel. Mark On Sat, Jul 21, 2018, 05:11 Soham Sarkar wrote: > I want to see the helix transition.. whether it is coming back or not in > the presence of the protecting osmolyte where urea is

Re: [gmx-users] (no subject)

I want to see the helix transition.. whether it is coming back or not in the presence of the protecting osmolyte where urea is already there in the system On Sat, 21 Jul 2018, 2:21 am Mark Abraham, wrote: > Hi, > > You haven't answered the question clearly. Do you care about observing the >

Re: [gmx-users] (no subject)

Hi, You haven't answered the question clearly. Do you care about observing the transition (whose properties will depend on how you introduce the mixing), or just the difference between before and after? Your proposed method is ill formed because you can't continue a simulation after fundamentally

Re: [gmx-users] (no subject)

Dear Krieger, Frankly speaking I am planning to run a REMD for 50ns with protein urea and water in it, then after 50ns I want to add a protecting osmolyte into the system and want to continue it for another 50ns REMD so that I can have the effect of the protecting osmolyte before and after adding

Re: [gmx-users] (no subject)

Dear Mark, Sorry for late reply of your queries. Frankly speaking I am planning to run a REMD for 50ns with protein urea and water in it, then after 50ns I want to add a protecting osmolyte into the system and want to continue it for another 50ns REMD so that I can have the effect of the

Re: [gmx-users] (no subject)

You can probably use gmx solvate for this with the frame at the end of 50 ns as input cp and a box of the new molecules as cs or possibly genion. We also have a tool for building simulation systems with small molecules called DruGUI http://prody.csb.pitt.edu/drugui/ although I don't know how you

Re: [gmx-users] (no subject)

Hi, Are you trying to observe something about the transition, or merely the different end points? Mark On Tue, Jul 10, 2018 at 4:12 PM Soham Sarkar wrote: > Dear all, > I am planning to do a simulation where after 50ns of simulation I want to > add some other chemicals in the system and

Re: [gmx-users] (no subject)

If you aren't adding anything too big, or to much of them, then take the final frame, use gmx insert-molecules (probably with a reduced vdw radius so they fit in) to put the additional molecule(s) in, perform standard pre production run energy minimisation etc, then off it goes again. Why can't

Re: [gmx-users] (no subject)

Also depends on what you try to do. Maybe Dry Martini? Look into:ARNAREZ, Clément, et al. Dry Martini, a coarse-grained force field for lipid membrane simulations with implicit solvent. Journal of chemical theory and computation, 2014, 11.1: 260-275. On Thursday, June 21, 2018, 5:22:15

Re: [gmx-users] (no subject)

Thank you, it worked. On Mon, May 14, 2018 at 3:43 PM, Mark Abraham wrote: > Hi, > > I don't know whether solvate supports such boxes, but if it does I would > use editconf first to describe the box, and then solvate to fill it. > Currently you are filling a cubic box

Re: [gmx-users] (no subject)

Hi, I don't know whether solvate supports such boxes, but if it does I would use editconf first to describe the box, and then solvate to fill it. Currently you are filling a cubic box and then transforming it to another shape, and that isn't a well formed operation. Mark On Mon, May 14, 2018 at

Re: [gmx-users] (no subject)

On 4/23/18 5:08 PM, rose rahmani wrote: Hi, I have a capped amino acid in box of water and ion(but the system is not charged) and named it initial.gro, i can see some unreal bonds when i open it with VMD(H atom has 2 bonds!). And when i open it with gaussview C and H atom where nonbobded and

Re: [gmx-users] (no subject)

Hi, Either your topology components are in the wrong order (like the message says) or you're doing something strange. Notice how your water won't have any atoms unless _FF_CHARMM is defined, which will only be defined if you've got a charmm force field involved. But nobody's got enough

Re: [gmx-users] (no subject)

> You need some ions to neutralise the system for long range electrostatics to work. This mostly applies to PME. However, because PME is basically *de facto* nowadays, it will most likely apply in most situations. However, I recently learned that PME can also be run with a non-neutral system, as

Re: [gmx-users] (no subject)

You need some ions to neutralise the system for long range electrostatics to work. We usually add more to make the simulation more like the real system (solution or cell). > On Jan 21, 2018, at 1:12 AM, Sankaran SV . <119013...@sastra.ac.in> wrote: > > Dear all, > >I am a beginer.

Re: [gmx-users] (no subject)

A beginner in what? Your question has nothing to do with Gromacs. Alex On 1/20/2018 11:12 PM, Sankaran SV . wrote: Dear all, I am a beginer. I would like to know the purpose of adding ions during the simulation process. -- Gromacs Users mailing list * Please search the

Re: [gmx-users] (no subject)

Thanks Justin I followed your suggestion. now I am able to restrain (immobile) any molecule during pulling. thanks for your help. On Tue, Jan 2, 2018 at 4:56 PM, Rakesh Mishra wrote: > Dear all > > I am just a beginner in gromacs. I have installed gromacs 5.1 version. I

Re: [gmx-users] (no subject)

You should give more details how you try to make residue 44 immobile. Keep in mind that some ways to do that can be "defeated" with strong enough pulling. Most likely you just have to try few times with different pulling and restraining options. On Tuesday, January 2, 2018, 12:30:59 PM

Re: [gmx-users] (no subject)

On 1/2/18 6:26 AM, Rakesh Mishra wrote: Dear all I am just a beginner in gromacs. I have installed gromacs 5.1 version. I If you're just starting out, don't use outdated software. Use the latest official version (2016.4) and be ready for a brand new 2018 release sometime soon. am

Re: [gmx-users] (no subject)

On 10/27/17 5:51 AM, saranya wrote: Dear Users, I have done a simulation of Aggregated amyloid beta peptide for 100ns. The pdb structure choosen for my work is 1IYT, which has several (10) model structures, but i have choosen only 4 structure for my simulation. The problem is after production,

Re: [gmx-users] (no subject)

use trjconv command with nojump option to center all the peptide. Use the starting structure as the starting configuration. regards, RC Dash On Fri, Oct 27, 2017 at 5:51 AM, saranya wrote: > Dear Users, > I have done a simulation of Aggregated amyloid beta peptide for

Re: [gmx-users] (no subject)

Thanks for the answering I have doubts , because in the gromacs manual , they have mentioned that , the application of Essential dynamics is also to enhance the sampling with respect to usual MD. So, i want to make sure whether my understanding about ED is correct or not ? On Oct 19, 2017 5:46

Re: [gmx-users] (no subject)

On 10/19/17 11:30 AM, Robert Nairn wrote: Yes I noticed the area per protein was displaying 0 from the output on the terminal. Having repeated the tutorial with my protein, i consistently get two messages that could be responsible. If i try to select start terminus as none (2) as per the

Re: [gmx-users] (no subject)

Yes I noticed the area per protein was displaying 0 from the output on the terminal. Having repeated the tutorial with my protein, i consistently get two messages that could be responsible. If i try to select start terminus as none (2) as per the tutorial I receive a message saying: Back Off! I

Re: [gmx-users] (no subject)

On 10/19/17 8:04 AM, Robert Nairn wrote: Dear all, I am currently trying to insert the MscL protein into the DMPC bilayer. I followed Justin Lemkul's tutorial 2 (with the exception of using dmpc instead of dppc) and receive this error message after shrinking and energy minimization.

Re: [gmx-users] (no subject)

Essential Dynamics = extracts the correlated motions of proteins to understand the motions that are most fundamental to the activity of the protein (http://www.gromacs.org/Documentation/How-tos/Essential_Dynamics) Accelerated MD = enhanced-sampling method that improves the conformational space

Re: [gmx-users] (no subject)

On 9/8/17 5:43 AM, abir paul wrote: hi, I am very new to gromacs. I want to see phosphorylation effect on a protein molecule. So I have phosphorylated my protein in charmm-gui server. when i tried to generate .gro file by using pdb2gmx command line it gives me following error :

Re: [gmx-users] (no subject)

I suggest check for the appropriate binding pocket. See whether the ligand relocates at some other point in protein or keep to stay away. Also check for the quality of the topology generated. On Wed, Aug 16, 2017 at 10:11 AM, wrote: > Hii Everyone > > I had performed a

Re: [gmx-users] (no subject)

Hi Iman, If I understand, you are planning on calculating the surface tension of water? To me, it seems odd that you would try to apply a surface-tension couple to your system, and then calculate the surface tension. Dan On Thu, Aug 10, 2017 at 5:42 AM, Iman Ahmadabadi

Re: [gmx-users] (no subject)

There is a minimum number of hydrogen bond formation (2 hydrogen bonds) in my protein-drug complex. I have a question about is there any influence of the drug in my protein-drug complex. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] (no subject)

Number of hydrogen bond depends on the nature of your drug. It can be zero, one or many. On Thu, Aug 10, 2017 at 10:33 AM, saranya wrote: > Hi, > I have done protein-drug simulations for 100ns. While calculating the > hydrogen bond between the protein-drug complex I am

Re: [gmx-users] (no subject)

I think it is all pretty simple, at least from what you are describe. If there are sufficient reason to believe that your membrane should be flat and not jagged, and your box size (supercell size, in the terminology you probably prefer) is properly set up, simply allow it to relax in vacuum at a

Re: [gmx-users] (no subject)

Dear Alex and Mark, Thank you for your kind reply. To begin with I am a Postdoc but with expertise is in DFT. It is my first venture into force field MD calculations. Hence, I am struggling. My group and the boss has similar expertise. So we have turned to public forums to ask questions. My

Re: [gmx-users] (no subject)

On 8/8/17 1:06 PM, Sorour Hasani wrote: Im working on simulating a CYP2D6 with its cofactors (heme ) with GROMACS. When I run pdb2gmx, using CHARMM27 FF, I had no error. After looking in the literature, I found their corresponding parameters: I added the following fields in CHARMM file

Re: [gmx-users] (no subject)

I did not quite understand your comment. However, I am trying my best to answer it. I have a surface MnO2 model. I have solvated the structure in all 3 directions. After that, I minimize it and run NVT simulation with the parameters as mentioned. However, I see that there is a deformation of

Re: [gmx-users] (no subject)

Hi, On the information given, nobody can tell whether the parameters you have for the interactions between Mn and O and maybe water are unsuitable, or that something is wrong with the method, or the initial conditions, or the code. Mark On Mon, 7 Aug 2017 23:11 gangotri dey

Re: [gmx-users] (no subject)

I did not quite understand your comment. However, I am trying my best to answer it. I have a surface MnO2 model. I have solvated the structure in all 3 directions. After that, I minimize it and run NVT simulation with the parameters as mentioned. However, I see that there is a deformation of the

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