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 >

[gmx-users] (no subject)

Hello! My name's FERIEL TERBECHE I am a genetic studant, from ALGERIA, Im preparing my last study's project (master degrees), wich is about hemophila A and factor VIII where I have to use gromacs, but, I don't know how to use it even I have it on my computer and unfortunately no one here can

[gmx-users] (no subject)

Hi, I've just installed GROMACS on Linux in Virtualbox. But, now I can't find my GROMACS, please tell me how to find it. Thank you. I've used these commands while installing gromacs:- sudo apt update sudo apt upgrade sudo apt install gcc sudo apt install cmake sudo apt install build-essential

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

[gmx-users] (no subject)

Hi, I have been a new user and i was following the protein-ligand complex tutorial for MD. I have used GROMOS96 54a7 FF and to build ligand topology i have used ATB webserver. I did download the .itp and .pdb file from there and converted that to .gro file. The problem i am facing is it shows an

[gmx-users] (no subject)

afsane_farh...@yahoo.com Sent from Yahoo Mail on Android -- 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)

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

[gmx-users] (no subject)

Hi all Can anyone help me with the DEFORM option in Gromacs to change the box values? -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 -- Gromacs Users mailing list * Please search the archive at

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

[gmx-users] (no subject)

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 ions.tpr :-) GROMACS -

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

[gmx-users] (no subject)

Dear Gromacs users I am running a free energy calculation of the protein-ligand complex. During the energy minimization process, I am getting many jumps in steps as below:- Step Time 1050010500.0 Energies (kJ/mol) Bond Restraint Pot. Angle

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

[gmx-users] (no subject)

Hi, i am trying to make the index file without loops and termini and using the option protein and ligand that is 1 and 13 but the index file is formed with the same as it is formed from the whole system. -- Kind Regards Nupur Munjal PhD Scholar (Bioinformatics) Department of Biotechnology &

[gmx-users] (no subject)

Dear All I am in trouble with gmx distance command. I want to calculate the distance between two amino acids (residue 130 and residue 153) in a protein after gromacs standard simulation. After generating of r130.ndx and r153.ndx index files, I use this command: gmx distance -f md_0_1_noPBC.xtc -s

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

[gmx-users] (no subject)

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 ins_prod_1.trr -o ins_prod_1.xtc -pbc cluster then for hydrogen bond correlation used following flag ::-gmx

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

[gmx-users] (no subject)

Dear All, I am doing a protein-ligand simulation, when i was try to *add ions to the system* gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr *there was an error* Fatal error: Syntax error - File lig.prm, line 2 Last line read: '[ bondtypes ]' Invalid order for directive bondtypes *my

[gmx-users] (no subject)

greetings everyone I was following protein ligand complex tutorial. EM run was fine even with double precision. Steepest Descents converged to Fmax < 1000 in 101 steps Potential Energy = -2.71399964872904e+06 Maximum force = 9.15885947946535e+02 on atom 4411 Norm of force =

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

[gmx-users] (no subject)

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 ends and the force field does not provide terminal entries or files. Fix your terminal

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

[gmx-users] (no subject)

I would like to calculate rmsd of protein system, but there is much time taking for trjcat of all simulated trajectories (.trr file) then generated .xtc file by using -center -pbc mol flag. from this .xtc file i use to calculate rms value by using flag g_rms -f .xtc -s .tpr -n .ndx -o .xvg I want

[gmx-users] (no subject)

Hi all, i am preparing system of DNA-protein complex, downloaded it from RCSB website, by using GROMACS force field AMBER03WS with water Model TIP4P (2005). The DNA chain contains DA, DT, DG, DC atom type. but the problem is that when i use command for energy minimization the following error

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)

Original message From: saranya Date: 01/11/2019 07:48 (GMT+01:00) To: gmx-us...@gromacs.org Subject: [gmx-users] (no subject) Hello everyone,while running nvt equilibration i am getting the error as:Step 12, time 0.024 (ps)  LINCS WARNINGrelative constraint deviation after

[gmx-users] (no subject)

Hello everyone, while running nvt equilibration i am getting the error as: Step 12, time 0.024 (ps) LINCS WARNING relative constraint deviation after LINCS: rms nan, max 92522.640625 (between atoms 217 and 218) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current,

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 >

[gmx-users] (no subject)

Dear gromacs users, Sorry for repeating my question. I didn't receive any email so I couldn't reply and I missed them. I am using following pull code in md simulation for pulling a ligand across the plasma membrane model. Ligand passes through the membrane,but along simulation, the size of

[gmx-users] (no subject)

Hi -- 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)

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

[gmx-users] (no subject)

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 unk.itp, line 497]: Duplicate atom index (23) in

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

[gmx-users] (no subject)

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. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] (no subject)

pradeepakumar...@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)

Dear user. I have a problem. I have to simulate a box of 100 molecules of polyvinylidene fluoride (PVDF) and 1436 molecules of the solvent ATBC. At first I built the single chain of PVDf and a single molecules of ATBC, and I was able to construct topology using opls force-field. The command that I

[gmx-users] (no subject)

Dear all, I have a protein_Ligand complex which I want  do Umbrella Sampling on it to find out free energy.for this purpose I used Justin tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ). | | | GROMACS Tutorial | | | Here is my questiones:in tutorial he said:

[gmx-users] (no subject)

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[gmx-users] (no subject)

ok -- 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)

* * * 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 addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received

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

be solved > > PS : next time add a title in you message. > > Good luck > > - > -- > > Message: 1 > Date: Fri, 5 Apr 2019 14:26:00 +0530 > From: Soham Sarkar > To: gmx-us...@gromacs.org >

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

+0530 From: Soham Sarkar To: gmx-us...@gromacs.org Subject: [gmx-users] (no subject) Message-ID: Content-Type: text/plain; charset="UTF-8" Dear all, I am using GROMACS-2018. I want to simulate a system which contain Tertiary Butyl alcohol (TBA) in it. I am facing problems while

[gmx-users] (no subject)

Dear all, I am using GROMACS-2018. I want to simulate a system which contain Tertiary Butyl alcohol (TBA) in it. I am facing problems while executing the GROMPP command. I have defined this residue in aminoacids.rtp. The error is like "NOTE 1 [file ions.mdp]: With Verlet lists the optimal

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

[gmx-users] (no subject)

Hi users, I have simulated a protein with gas molecules (CO2,NO2 and SO2) for 100ns. I have followed the protein ligand tutorial. I have applied position constraints. After equilibrium the gas molecules are at the docked position but at the 60ns simulation the gas molecules are far away

[gmx-users] (no subject)

Dear all I encountered with following error when running the umbrella sampling simulation of a protein. What modification should I make in the pull code to get rid of the error. ERROR 1 [file npt_umbrella.mdp]: When the maximum distance from a pull group reference atom to other atoms in the

[gmx-users] (no subject)

Dear Gromacs users, I would like to buy a videocard for calculation on GPU. I choose between RTX 2080Ti and Titan Xp. Please, tell me which videocard to choose? -- Искренне Ваш, Никита Шалин -- Gromacs Users mailing list * Please search the archive at

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 ,

[gmx-users] (no subject)

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 , newbox.mdp , npt.mdp , nvt.mdp , porse.itp , topol.top input files for molecular simulation of my molecule. Please teach me how can I generate or create all the above

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

[gmx-users] (no subject)

Hello Everyone, I want to calculate some properties of the solvent molecules within 6angstrom from the protein backbone, for that I need a index group which only contain that number of solvent molecules in the index.ndx file so that I can specifically select that index to calculate different

[gmx-users] (no subject)

Hello Everyone, I want to calculate some properties of the solvent molecules within 6angstrom from the protein backbone, for that I need a index group which only contain that number of solvent molecules in the index.ndx file so that I can specifically select that index to calculate different

[gmx-users] (no subject)

-- 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)

Hello GMX users, I have old simulation trajectories (.xtc) with their topologies (.tpr). Is there any way to get energy files (.edr) without rerun the simulations? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] (no subject)

ERROR 1 [file res.itp, line 57]: Invalid Atomnr j: 4, b2->nr: 3 I am getting the above error for the command gmx grompp -f em.mdp -c solv.gro -p topol1.top -o ions.tpr. My res.itp file is given below. I couldnot understand the meaning of this error. Can you please help me? part of the .itp is

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

[gmx-users] (no subject)

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 [TPPREV_jun16] WAS NOT " I gave the command

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,

[gmx-users] (no subject)

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, it gives error saying the following Command

[gmx-users] (no subject)

Dear GMX users, I would like to share a difficulty installing GROMACS/2018.3 with you. I use GCC/6.4.0 on a Linux cluster with CentOS 7.5 kernel and GPU nodes equipped with 4 x P100 Nvidia devices. Below is the cmake configuration that I use, followed by the error that I receive. I am not sure

[gmx-users] (no subject)

Dear Justin its your conversation regarding pulling of dsDNA. Because gromacs is replying as there message is too big so cant be send and due to that I can not replied in orginal conversation. But I want to start from the last conversation. from your side "It seems to me you have two steps to

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

[gmx-users] (no subject)

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. -- Gromacs Users mailing list * Please search

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

[gmx-users] (no subject)

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 searched it among publications but I didn't find it at all. Best regards, -- *** Sako

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:

[gmx-users] (no subject)

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, but the atom H used in an interaction of type

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

[gmx-users] (no subject)

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 accordingly as mentioned in the tutorials. While running grompp command, I get following error: gmx grompp -f em.mdp -c

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

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