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

[gmx-users] (no subject)

Hi every body can any one explain what is the mean of this graph obtained from gromacs constant velocity pulling of dsDNA along the helical direction. (force.xvg). Basically sudden drop of force represents what ? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] (no subject)

Hi every body can any one explain what is the mean of this graph obtained from gromacs constant velocity pulling of dsDNA along the helical direction. (force.xvg). Basically sudden drop of force represents what ? -- -- Gromacs Users mailing list * Please search the archive at

[gmx-users] (no subject)

Dear gromacs user. What should be the value of spring constant (k) and rate if one wants to pull dsDNA (say bDNA of 16 bp ) surrounded by aqua (water model) during pulling using umbrella sampling . -- *With Best-Rakesh Kumar Mishra* * (RA)CSD SINP Kolkata, India* *E-mail -

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

[gmx-users] No subject

Hello everybody, I am sending this email again to ask about orientation restraints in gromacs, in the manual it says that when writing the orientation restraints section in the topology file, one of the fields represent the constant c in the RDC equation, and the value for N-H vector are given

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

[gmx-users] (no subject)

I have a blade server now. Want to install Gromacs. Our lab studies have used version 4.6.3. We would like to continue and to compare with previous studies. So will it be ok to install this old version or new version 5? Because comarison would make no sense if we use new version. -- Gromacs

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

[gmx-users] (no subject)

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 continue it for another 50ns, so that I can have the effect of that chemicals exclusively before and after adding it to the system.Is it at all possible? If yes please

[gmx-users] (no subject)

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 continue it for another 50ns, so that I can have the effect of that chemicals exclusively before and after adding it to the system.Is it at all possible? If yes please

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

[gmx-users] (no subject)

I want to perform MD simulation using groamcs in implicit solvent. Can you help me which force field is compatible with which solvent I can take? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] (no subject)

Hello, Can anyone provide me the topology for Adenosine Monophosphate Molecule (AMP)for Gromacs (gromos54a7 forcefield). Thanks Nikita Bora * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named

[gmx-users] (no subject)

Dear all, How to modify a mdp file to generate two different tpr files, from the same initital coordinates of a Na 1.5 voltage gated channel in the membrane (it is already relaxed and in a closed state)? I need to set parameters for the system with a voltage of -80 mV and than, after 100 ns start

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

[gmx-users] (no subject)

Hello all, I modeled a hexagonal box of water using the following steps: gmx solvate -cs spc216.gro -o waterst1 -box 6 6 6 gmx editconf -f waterst1.gro -o w120.gro -bt tric -box 4.5 4.5 5.56 -angles 90 90 120 -c After which i used trjconv with -pbc atom -ur compact and obtained the hexagonal

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

[gmx-users] (no subject)

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 were single atoms around remained bonded

[gmx-users] (no subject)

Hi all, How can I convert 3 different gromacs itp file to generate single psf file ? Is there any command to do that I tried using top2psf.pl script to do that , but it failed. Thank you. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] (no subject)

Dear gromacs users, can any one please tell me that how we get the secondary structure propensity or secondary structure content(%) as a function of simulation time. I used "gmx do_dssp" but it gives me number of residues forming the secondary structure vs simulation time. is it same thing or

[gmx-users] (no subject)

Dear users and developers! I have a question about replica exchange sampling and simulation annealing method. Well, I have a protein (TubulinG) X-ray, however it lack last 10-11 residues, which are probably exposured to the solvent (and it seems are flexible enough to be invisible for X-ray). The

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

[gmx-users] (no subject)

Dear all l am using gromacs 4.5.5 version for simulation carbon nanotubes with charmm27 force feild ,there was no error grompp stage,but when l do simulation of carbon nanotube in tip3p water encountered with fatal error: [ file tip3p.itp, line 40]: Atom index (1) in settles out of bounds

[gmx-users] (no subject)

hi . i am doing simulation of peptide in DOPC bilayer. i have dopc.itp , dopc.pdb, dopc.gro , peptide.itp , sample.top for dopc , peptide.pdb,topol.top. i used below commands. gmx editconf -f peptide.gro -o pep.gro -box 6.35172 6.80701 7.49241 -c (it corresponds to the x/y/z box vectors of

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

[gmx-users] (no subject)

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 archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

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

[gmx-users] (no subject)

Dear all I am just a beginner in gromacs. I have installed gromacs 5.1 version. I am doing pulling for si-rna (double stranded, 22 nucleotides each ). I am applying pulling code of umbrella sampling. Using that, we have chosen 22nd number residue of chain A is under pulling with constant

[gmx-users] (no subject)

Dear sir I am just a beginner in gromacs. I have installed gromacs 5.1 version. I am doing pulling for si-rna (double stranded, 22 nucleotides each ). I am applying pulling code of umbrella sampling. Using that, we have chosen 22nd number residue of chain A is under pulling with constant

[gmx-users] (no subject)

Hi, I have a simple system of non-charged diatomic molecule, (A-B). I expect total LJ interaction energy in such system when we put LJ parameters of atom B zero (c6 and c12=0) should be equal with total LJ energy of a system containing only atom A. Am I right? Best regards -- Gromacs Users

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

[gmx-users] (no subject)

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, if i check the final .gro files of md

[gmx-users] (no subject)

Dear all, I want to use GMX to simulate ethanol solution interaction with macromolecular in a polarizable force filed. Whether the macromolecular and ethanol PDB files need adding Drude particles? and how to produce an ethanol.itp file for Drude2013 force field? Do the Drude2013

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.

[gmx-users] (no subject)

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. [christos@chpc-cp39 Simulation]$ gmx mdrun -v

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

[gmx-users] (no subject)

Hi all, I have a very basic question about essential dynamics. I want to know whether essential dynamics function is similar to Accelerated MD ? Or essential dynamics is different from Accelerated MD ? Thanks in advance. Kingsleg Theras -- Gromacs Users mailing list * Please search the archive

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 :

[gmx-users] (no subject)

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 : Fatal error: Residue

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

[gmx-users] (no subject)

Hii Everyone I had performed a 100ns protein-ligand (docked complex) simulation with gromacs 5.1.4. The ligand in my case is hydrogen peroxide. I have removed the PBC effect and centered the protein. I have used the following commands: gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o

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

[gmx-users] (no subject)

Dear Users, I'm determining my .mdp file for NPT equilibration, but I don't know how to determine the ref_p section of mdp. pcoupl = berendsen pcoupltype = surface-tension tau_p = 0.5 0.5 ref_p = 1.0 1.0 compressibility = 4.46e-5 4.46e-5 I'm gonna to calculate surface tension for a layer of

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

[gmx-users] (no subject)

Hi, I have done protein-drug simulations for 100ns. While calculating the hydrogen bond between the protein-drug complex I am getting only 2 hydrogen bonds. I just want to clarify that 2 hydrogen bonds mean very low, is it acceptable to get this minimum number of bond formation for the protein

[gmx-users] (no subject)

Hi, I have done protein-drug simulations for 100ns. While calculating the hydrogen bond between the protein-drug complex I am getting only 2 hydrogen bonds. I just want to clarify that 2 hydrogen bonds mean very low, is it acceptable to get this minimum number of bond formation for the protein

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

[gmx-users] (no subject)

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 ffbonded.itp [ bondtypes ] ; i j func b0 kb SG FE 1

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

Re: [gmx-users] (no subject)

Hi, Are you trying to implement a model that you know is capable of produce a surface that does not deform in unexpected ways? Mark On Mon, 7 Aug 2017 16:35 gangotri dey wrote: > Dear all, > > I am trying to equilibrate a MnO2 surface (not cluster but periodic). I > have

[gmx-users] (no subject)

Dear all, I am trying to equilibrate a MnO2 surface (not cluster but periodic). I have solvated the surface with water in all 3 directions. After the NVT run, I see that the surface is deformed. I was wondering what else can I add in my nvt.mdp to not encounter this problem? I have mainly

[gmx-users] (no subject)

Thanks a lot！ In fact, I just can not confirm the value of pconc or nconc of the polar.mdp, namely under what conditions should I set “0” or “0.150”？ *Yours sincerely* *Yujie, liu* -- Gromacs Users mailing list * Please search the archive at

[gmx-users] (no subject)

Hi all, I was trying to simulate a protein-DNA complex using gromos54a7 forcefield. The error comes as, Fatal error: Residue 'DA' not found in residue topology database Clearly, it is not finding the DA residue in its database. How can I solve this? Thanks, Souparno Adhikary, CHPC Lab,

[gmx-users] (no subject)

jivesh.mad...@gmail.com -- 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 requests visit

[gmx-users] (no subject)

e-Layer Hexagonal Boron-Nitride. Materials Research Letters 1, 200-206, doi:10.1080/21663831.2013.824516 (2013). Best, Jason Message: 5 Date: Wed, 12 Jul 2017 19:12:26 -0600 From: Alex <nedoma...@gmail.com> To: Discussion list for GROMACS users <gmx-us...@gromacs.org> Subject: Re: [

Re: [gmx-users] (no subject)

Hi, You need to have a file that contains the frame you want to start from, and give that to gmx grompp -t Mark On Wed, Jul 12, 2017 at 5:54 PM CLARK NICOLAS Joan wrote: > Dear gmx users, > > > I am trying to extend a finished simulation from a frame which is not the

[gmx-users] (no subject)

Dear gmx users, I am trying to extend a finished simulation from a frame which is not the last one in my trajectory. I have tried convert-tpr but I think it's only modifying the number of steps because the resulting tpr file starts the simulation from the first or the last frame depending on

Re: [gmx-users] (no subject)

Hi, You can't do that with normal gromacs. But googling may reveal options. Mark On Sat, 8 Jul 2017 14:07 Shivangi Agarwal wrote: > hello to all > > How can i perform PBSA in gromacs > > > Thanks in advance > -- > Gromacs Users mailing list > > * Please search

[gmx-users] (no subject)

hello to all How can i perform PBSA in gromacs Thanks in advance -- 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

[gmx-users] (no subject)

1 F -- 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 requests visit

Re: [gmx-users] (no subject)

Anyone if have idea, Kindly address On 28 Jun 2017 07:41, "Shivangi Agarwal" wrote: > Dear all gromacs users > > i have to define a new residue, i have added it in *residuetype.dat* file. > but still getting error: "residue type not found". > Kindly suggest > -- >

[gmx-users] (no subject)

Dear all gromacs users i have to define a new residue, i have added it in *residuetype.dat* file. but still getting error: "residue type not found". Kindly suggest -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] (no subject)

Hi, I suggest you ask the authors of the tools, having checked their documentation. Mark On Wed, Jun 21, 2017 at 6:36 AM Shivangi Agarwal < shivangi.agarwal...@gmail.com> wrote: > Hello all > > How to handle HS14 generated by ATB server in topology file? > > > Regards > -- > Gromacs Users

Re: [gmx-users] (no subject)

Hi, On Wed, Jun 21, 2017 at 4:32 PM Shivangi Agarwal < shivangi.agarwal...@gmail.com> wrote: > Hi > But it is broken. .. > Nope, it's just in one of the infinite number of equivalent representations of the same thing ;-) mdrun doesn't know that you want it to write a file where your protein and

Re: [gmx-users] (no subject)

Hi But it is broken. .. strand with proline with three odr residues has been broken and visible... i have Checked in vmd and pymol On 21 Jun 2017 17:16, "Mark Abraham" wrote: > Hi, > > On Wed, Jun 21, 2017 at 1:21 PM Shivangi Agarwal < > shivangi.agarwal...@gmail.com>

Re: [gmx-users] (no subject)

Hi, On Wed, Jun 21, 2017 at 1:21 PM Shivangi Agarwal < shivangi.agarwal...@gmail.com> wrote: > Hello to all gmx users > > I am performing protein ligand complex MD simulation but my protein > structure has been broken during energy minimization process. > It's not broken, but rather in an

[gmx-users] (no subject)

Hello to all gmx users I am performing protein ligand complex MD simulation but my protein structure has been broken during energy minimization process. What may be the suitable reason? How I can solve this? Your support is highly appreciated -- Gromacs Users mailing list * Please search the

[gmx-users] (no subject)

Hello all How to handle HS14 generated by ATB server in topology file? Regards -- 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

Re: [gmx-users] (no subject)

Thanks sir for your support. Dear justin sir do u hv any more ideas On 20 Jun 2017 18:54, "Mark Abraham" wrote: > Hi, > > Follow ATB's directions for how to use the files it produces. If ATB is > creating a new atom type, then it will be supplying parameters that

Re: [gmx-users] (no subject)

Hi, Follow ATB's directions for how to use the files it produces. If ATB is creating a new atom type, then it will be supplying parameters that belong in the [atomtypes] directive, and their site needs to give you instructions for how to get those recognized. Search their website and ask on their

Re: [gmx-users] (no subject)

Thanks for your suggestion. One more thing In topology file generated by ATB, there is HS14 atomtype and i am getting error FATAL error ATomtype HS14 not found How to handle this error? Kindly suggest On Tue, Jun 20, 2017 at 12:18 PM, Mark Abraham wrote: > Hi, > >

Re: [gmx-users] (no subject)

Hi, You don't need a file in the gro format. You need coordinates that match the topology present in any supported file format, eg pdb or g96 etc. Mark On Tue, 20 Jun 2017 09:01 Shivangi Agarwal wrote: > Hello > > I used the ATB server for generation of topology

[gmx-users] (no subject)

Hello I used the ATB server for generation of topology file following Gromacs Turorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html

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