Re: [gmx-users] Protein-Ligand Interaction calculation

On 2/17/20 7:18 AM, Peter Mawanga wrote: Hello everyone I used the CHARMM-GUI Membrane Builder to build a bilayer around my protein-ligand complex. However, unfortunately the ligand was not mentioned separately in the index (.ndx) file although it was mentioned in the topology (.top) file. H

Re: [gmx-users] Protein-Ligand Interaction calculation

Hi.. You have to specify energy groups in .mdp option..then rerun the simulation..and analyse with gmx energy command On Mon 17 Feb, 2020, 5:52 PM Александр Лашков, wrote: > You can rebuild index file using gmx make_ndx gromacs util. > Alex > > пн, 17 февр. 2020 г. в 15:19, Peter Mawanga

Re: [gmx-users] Protein-Ligand Interaction calculation

You can rebuild index file using gmx make_ndx gromacs util. Alex пн, 17 февр. 2020 г. в 15:19, Peter Mawanga : > Hello everyone > > I used the CHARMM-GUI Membrane Builder to build a bilayer around my > protein-ligand complex. > > However, unfortunately the ligand was not mentioned separately in t

[gmx-users] Protein-Ligand Interaction calculation

Hello everyone I used the CHARMM-GUI Membrane Builder to build a bilayer around my protein-ligand complex. However, unfortunately the ligand was not mentioned separately in the index (.ndx) file although it was mentioned in the topology (.top) file. Hence I am not able to calculate the energy bet

Re: [gmx-users] Protein ligand simulation topology

On 10/8/19 7:30 AM, DEEPANSHU SINGLA wrote: Respected sir/mam, While doing the simulation of my protein with a ligand I received the following error: Fatal Error: No line with moleculetype 'SOL' found in the [molecules] section of the 'topol.top' Molecule section of my topology file is as f

[gmx-users] Protein ligand simulation topology

Respected sir/mam, While doing the simulation of my protein with a ligand I received the following error: Fatal Error: No line with moleculetype 'SOL' found in the [molecules] section of the 'topol.top' Molecule section of my topology file is as follows: [molecules] ; Compound#mols Prot

[gmx-users] Protein ligand simulation

Respected sir/mam, During ligand topology generation I received the following error: Please be sure to use the same version of CGenFF in your simulation that was used during parameter generation: --version of CGenFF detected in charmm36-mar2019.ff/forcefield.doc : 4.1 WARNING: cGenFF versions ar

Re: [gmx-users] Protein ligand simulation

On 10/1/19 3:39 AM, DEEPANSHU SINGLA wrote: I am trying to learn protein ligand simulation. I tried to follow the steps for lysozyme using the GROMACS tutorial. I received the following error: *ERROR 1 {file jz4.itp, line 183]:* * No default Proper Dih. types* *ERROR 2 [file jz4.itp, line 1

Re: [gmx-users] Protein ligand simulation

you should follow steps from protein-Ligand simulation. Write in google " www.bevanlab.biochem.vt.edu › justin › gmx-tutorials › complex_old ". Take coordinates of JZ4 from PRODRG.

[gmx-users] Protein ligand simulation

I am trying to learn protein ligand simulation. I tried to follow the steps for lysozyme using the GROMACS tutorial. I received the following error: *ERROR 1 {file jz4.itp, line 183]:* * No default Proper Dih. types* *ERROR 2 [file jz4.itp, line 194]:* * No default Proper Dih. types* *Fatal err

Re: [gmx-users] Protein ligand simulation

First of all take coordinates of ligand from online available resources mentioned in protocol of protein ligand simulation and exactly follow the same you will get simulation run Regards Najam On Sat, Sep 28, 2019, 2:38 PM DEEPANSHU SINGLA wrote: > I am trying to learn protein ligand simulatio

[gmx-users] Protein ligand simulation

I am trying to learn protein ligand simulation. I tried to follow the steps for lysozyme using the GROMACS tutorial. I received the following error: *ERROR 1 {file jz4.itp, line 183]:* * No default Proper Dih. types* *ERROR 2 [file jz4.itp, line 194]:* * No default Proper Dih. types* *Fatal err

[gmx-users] protein-ligand simulation problem

Hi Gromacs Users, I am trying to protein-ligand simulation where I have 12 protein and 12 ligand molecules. Minimization step went perfectly well and the system got minimized less than 2 steps. However, it is becoming unstable once I am trying to do real simulation. I am trying to equilibrate

Re: [gmx-users] Protein-Ligand interactions

Hi Use higher force constant and see what is happening On Tue 16 Apr, 2019, 6:14 PM RAHUL SURESH On Tue, Apr 16, 2019 at 1:57 PM Bratin Kumar Das < > 177cy500.bra...@nitk.edu.in> wrote: > > > Hi, > > The force you assigned for position restrain may not be enough to > hold > > the ligand i

Re: [gmx-users] Protein-Ligand interactions

On Tue, Apr 16, 2019 at 1:57 PM Bratin Kumar Das < 177cy500.bra...@nitk.edu.in> wrote: > Hi, > The force you assigned for position restrain may not be enough to hold > the ligand in the proper position. If u follow the gromacs tutorial ...the > simulation method is not wrong. > Thank you. I a

Re: [gmx-users] Protein-Ligand interactions

Hi, The force you assigned for position restrain may not be enough to hold the ligand in the proper position. If u follow the gromacs tutorial ...the simulation method is not wrong. On Tue 16 Apr, 2019, 11:22 AM RAHUL SURESH Hi Users. > > A basic clarification on protein and small molecule in

[gmx-users] Protein-Ligand interactions

Hi Users. A basic clarification on protein and small molecule interaction. I have a docked complex of a protein-ligand (to accept, the docking score is too low). On simulation, even after applying position restraint, I find the ligand moving around the protein. Is this because there is any error

[gmx-users] protein-ligand analysis

Hi all How can I find the chains interacting, forming H-bonds and hydrophobic interactions after a protein-ligand simulation? I tried VMD but there seems not to be good options to characterize them all. Is it possible to do such analysis in VMD or Gromacs and how? Thanks. -- Gromacs Users maili

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

On Thu, Dec 20, 2018 at 10:05 AM Prasanth G, Research Scholar < prasanthgha...@sssihl.edu.in> wrote: > Dear Sir, > > Thanks a lot for the inputs. I tried incorporating the forcefield > parameters (directory) obtained from the atbserver in the working > directory. When i was trying to convert the p

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

Dear Sir, Thanks a lot for the inputs. I tried incorporating the forcefield parameters (directory) obtained from the atbserver in the working directory. When i was trying to convert the protein.pdb to .gro, I noticed that the forcefield showed up in the menu as one included in local directory, jus

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

On Wed, Dec 19, 2018 at 4:34 AM Prasanth G, Research Scholar < prasanthgha...@sssihl.edu.in> wrote: > Dear Sir, > > I am running GROMACS 5.1.4 on a server. > I had converted the protein(pdb2gro) using the latest GROMOS forcefield. > As per your suggestion, I had downloaded the parameter files from

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

Dear Sir, I am running GROMACS 5.1.4 on a server. I had converted the protein(pdb2gro) using the latest GROMOS forcefield. As per your suggestion, I had downloaded the parameter files from ATB server. As per the readme file from the server (in the parameters folder), i had updated my topol.top lik

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

On Tue, Dec 18, 2018 at 12:17 AM Sri Prasanth Ghanta, Doctoral Research Scholar, Biosciences, SSSIHL wrote: > Dear all, > > I have started following the new tutorial > and the old tutorial > < > http://www.bevanlab.biochem.vt.edu/Pages/Personal/

[gmx-users] Protein-ligand complex simulation and ATBserver file

Dear all, I have started following the new tutorial and the old tutorial to carryout the simulation of JZ4 with Lysozyme. I was unable to run the cgen

Re: [gmx-users] Protein-Ligand in bilayer

Hi Dr. Mark I have already posted in the respective forum. I am just looking for some alternative method or to know if I am doing it wrong.! But anyway I overcame this error. After docking, add respective hydrogens and save it as mol2 file. Make it as complex with protein and save as PDB. These

Re: [gmx-users] Protein-Ligand in bilayer

Hi, None of those are GROMACS tools, so you will probably do better asking elsewhere. But why not generate the topology after the ligands atoms get sorted? Mark On Sat, Aug 11, 2018, 04:18 RAHUL SURESH wrote: > Hi Dr. Mark. > > The docked complex ( docked using auto dock ) when given as input

Re: [gmx-users] Protein-Ligand in bilayer

Can anyone explain the right procedure to be followed while building protein-ligand-popc bilayer? On Sat, Aug 11, 2018 at 6:48 AM RAHUL SURESH wrote: > Hi Dr. Mark. > > The docked complex ( docked using auto dock ) when given as input in > charmm-gui, it ask for either mol2 file or top and prm f

Re: [gmx-users] Protein-Ligand in bilayer

Hi Dr. Mark. The docked complex ( docked using auto dock ) when given as input in charmm-gui, it ask for either mol2 file or top and prm file generated using paramchem. But then it shows some atom number mismatch and couldn’t proceed further. The docked ligand ( pdbqt ) is converted to pdb form

Re: [gmx-users] Protein-Ligand in bilayer

Hi, Does CHARMM-GUI not provide a output coordinate file that matches the generated topology file? I don't know why you find its change of ordering a problem. Mark On Thu, Aug 9, 2018, 18:48 RAHUL SURESH wrote: > Hi users. > > It look so complicated to carry out a protein ligand simulation in

Re: [gmx-users] Protein-Ligand in bilayer

For simulations using the Charmm36 params, using CHARMM-GUI is recommended. Otherwise, you can also check out Justin's tutorial which is quite instructive for beginners and provides a step by step method to build a membrane protein system. On Fri, Aug 10, 2018 at 2:24 PM, RAHUL SURESH wrote: > T

Re: [gmx-users] Protein-Ligand in bilayer

Thank you. I wanna know of the alternative method to carry out this simulation. other than using charmm gui. thank you On Fri, Aug 10, 2018 at 2:07 PM, Abhishek Acharya wrote: > I see. I have not used charmm-gui for building system as complex as yours, > so I can't comment on the issue. But thi

Re: [gmx-users] Protein-Ligand in bilayer

I see. I have not used charmm-gui for building system as complex as yours, so I can't comment on the issue. But this is a problem specific to charmm-gui. I suggest you contact the authors of the web-service directly. Abhishek On Fri, Aug 10, 2018 at 10:07 AM, RAHUL SURESH wrote: > Hi. > > Thank

Re: [gmx-users] Protein-Ligand in bilayer

Hi. Thank you. But the system (protein ligand) is being constructed in charm gui input generator, where it automatically compare the complex pdb and ligand mol2 file ( which will Ben uploaded ). On Thu, 9 Aug 2018 at 11:24 PM, Abhishek Acharya wrote: > Hi, > > > > > It look so complicated to c

Re: [gmx-users] Protein-Ligand in bilayer

Hi, > It look so complicated to carry out a protein ligand simulation in Lipid > bilayer system using charmm ff. I have a ligand with 27 atoms ( includes > Hydrogen ). The initial structure (monomer) is simulated in popc > constructed using charmm gui web page. To construct the same for the > p

[gmx-users] Protein-Ligand in bilayer

Hi users. It look so complicated to carry out a protein ligand simulation in Lipid bilayer system using charmm ff. I have a ligand with 27 atoms ( includes Hydrogen ). The initial structure (monomer) is simulated in popc constructed using charmm gui web page. To construct the same for the portein

Re: [gmx-users] protein ligand faraway from one another

3:11 AM, Du, Yu wrote: -Original Messages- From: "Fakhar Alam" Sent Time: 2017-09-28 16:07:52 (Thursday) To: gmx-us...@gromacs.org Cc: Subject: [gmx-users] protein ligand faraway from one another Dear Gromacs Experts, I am doing simulation of protein-ligand complex. Ho

Re: [gmx-users] protein ligand faraway from one another

e looking at > the protein-ligand complex tutorial :) > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx > -tutorials/complex/index.html > > -Justin > > > On Thu, Sep 28, 2017 at 3:11 AM, Du, Yu wrote: >> >> >>> >>> -----Original Mes

Re: [gmx-users] protein ligand faraway from one another

day) To: gmx-us...@gromacs.org Cc: Subject: [gmx-users] protein ligand faraway from one another Dear Gromacs Experts, I am doing simulation of protein-ligand complex. However when I follow the steps in the tutorial, the ligand is very faraway from the protein. How can I put the ligand close

Re: [gmx-users] protein ligand faraway from one another

t; From: "Fakhar Alam" > > Sent Time: 2017-09-28 16:07:52 (Thursday) > > To: gmx-us...@gromacs.org > > Cc: > > Subject: [gmx-users] protein ligand faraway from one another > > > > Dear Gromacs Experts, > > > > I am doing simulation of protein-ligan

Re: [gmx-users] protein ligand faraway from one another

> -Original Messages- > From: "Fakhar Alam" > Sent Time: 2017-09-28 16:07:52 (Thursday) > To: gmx-us...@gromacs.org > Cc: > Subject: [gmx-users] protein ligand faraway from one another > > Dear Gromacs Experts, > > I am doing simulation o

[gmx-users] protein ligand faraway from one another

Dear Gromacs Experts, I am doing simulation of protein-ligand complex. However when I follow the steps in the tutorial, the ligand is very faraway from the protein. How can I put the ligand close to the protein ? Thanks, Alam -- Gromacs Users mailing list * Please search the archive at http://

Re: [gmx-users] protein -ligand complex dissociating during simulation

Dear Rahul and Justin Thanks for the suggestion, I will check the parameterisation once more. Regards Sneha On Sat, Jul 22, 2017 at 7:05 AM, RAHUL SURESH wrote: > On Sat, 22 Jul 2017 at 2:47 AM, Justin Lemkul wrote: > > > > > > > On 7/21/17 10:56 AM, RAHUL SURESH wrote: > > > It sounds like s

Re: [gmx-users] protein -ligand complex dissociating during simulation

On Sat, 22 Jul 2017 at 2:47 AM, Justin Lemkul wrote: > > > On 7/21/17 10:56 AM, RAHUL SURESH wrote: > > It sounds like some internal dihedral problem. Request you, check on it. > > > > How did you deduce that? Dear Justin I faced the similar kind of problem. Visualisation Of my trajectory help

Re: [gmx-users] protein -ligand complex dissociating during simulation

On 7/21/17 10:56 AM, RAHUL SURESH wrote: It sounds like some internal dihedral problem. Request you, check on it. How did you deduce that? Indeed, conformational sampling may be an issue, so one should check the internal geometries of the ligands, preservation of various interactions with

Re: [gmx-users] protein -ligand complex dissociating during simulation

It sounds like some internal dihedral problem. Request you, check on it. On Fri, 21 Jul 2017 at 6:54 PM, Sneha Vishwanath < snehavishwanat...@gmail.com> wrote: > @ Justin: I have re-imaged the trajectory with trjconv using and still the > ligand dissociates from one of the chain but remain bound

Re: [gmx-users] protein -ligand complex dissociating during simulation

@ Justin: I have re-imaged the trajectory with trjconv using and still the ligand dissociates from one of the chain but remain bound with the other chain. @ Gangotri: I am not sure how constraining the bond between protein might help. Can you please elaborate if possible. Thanks in advance. Sne

Re: [gmx-users] protein -ligand complex dissociating during simulation

On 7/21/17 8:56 AM, Sneha Vishwanath wrote: Dear all I am simulating a dimeric protein, with each subunit bound to a small molecule. During the simulation, one of the ligands is dissociating from the chain and moving all around the chain while the same ligand remains bound to the chain during

Re: [gmx-users] protein -ligand complex dissociating during simulation

Hey! You might want to constrain the bond between the 2 protein chains. G *Thank you* *Gangotri Dey* Postdoctoral Associate Rutgers University New Brunswick Chemistry and Chemical Biology 174 Frelinghuysen Road, Piscataway, NJ 08854 Phone: +16092162254 On Fri, Jul 21, 2017 at 8:56 AM, Sne

[gmx-users] protein -ligand complex dissociating during simulation

Dear all I am simulating a dimeric protein, with each subunit bound to a small molecule. During the simulation, one of the ligands is dissociating from the chain and moving all around the chain while the same ligand remains bound to the chain during simulation. Experiments show that the ligand bin

Re: [gmx-users] Protein-ligand binding Cut-offs

lf Of Mark Abraham Sent: 28 June 2017 15:13 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-ligand binding Cut-offs Hi, You get to choose... do you want everything within some distance of the protein center of mass, or any protein atom, or something else. But don't be suprrised if ther

Re: [gmx-users] Protein-ligand binding Cut-offs

mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 28 June 2017 11:34 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > How are you interpreting "within 4A of my protein?" What has your >

Re: [gmx-users] Protein-ligand binding Cut-offs

sys.kth.se] On Behalf Of Mark Abraham Sent: 28 June 2017 11:34 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-ligand binding Cut-offs How are you interpreting "within 4A of my protein?" What has your protein's center of mass got to do with it? Mark On Wed, Jun 28

Re: [gmx-users] Protein-ligand binding Cut-offs

--Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 28 June 2017 11:08 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs >

Re: [gmx-users] Protein-ligand binding Cut-offs

: Re: [gmx-users] Protein-ligand binding Cut-offs Is the radius of your protein greater than 0.4 nm? Mark On Wed, 28 Jun 2017 12:05 Pandya, Akash wrote: > Hi, > > I want to select all the ligands in my box within 4A of my protein. I > looked at gmx help select and I used the comma

Re: [gmx-users] Protein-ligand binding Cut-offs

f group "1"' > > Many thanks, > > Akash > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 21 June 2017 11:56 > To: gmx-u

Re: [gmx-users] Protein-ligand binding Cut-offs

mx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 21 June 2017 11:56 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-ligand binding Cut-offs Hi, You aren't getting output because you aren't actually making a selection - see "gmx help select" an

Re: [gmx-users] Protein-ligand binding Cut-offs

gt; -seltype dyn_mol_com -pdbatoms all > > Akash > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 16 June 2017 17:22 > To: gmx-us...@gr

Re: [gmx-users] Protein-ligand binding Cut-offs

-seltype dyn_mol_com -pdbatoms all Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 16 June 2017 17:22 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-ligand b

Re: [gmx-users] Protein-ligand binding Cut-offs

rom: "Mark Abraham" To: "gmx-users" Sent: Tuesday, June 20, 2017 8:40:33 PM Subject: Re: [gmx-users] Protein-ligand binding Cut-offs Hi, No, that's not a prerequisite, but it is one approach. Mark On Tue, Jun 20, 2017 at 8:16 PM Pandya, Akash wrote: > H

Re: [gmx-users] Protein-ligand binding Cut-offs

> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 16 June 2017 17:22 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > Hi, > &

Re: [gmx-users] Protein-ligand binding Cut-offs

17:22 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-ligand binding Cut-offs Hi, Gmx select will produce a selection eg of all molecules with an atom within a cutoff of any atom in another molecule. Mark On Fri, 16 Jun 2017 18:15 Pandya, Akash wrote: > Hi all, > > I h

Re: [gmx-users] Protein-ligand binding Cut-offs

Hi, Gmx select will produce a selection eg of all molecules with an atom within a cutoff of any atom in another molecule. Mark On Fri, 16 Jun 2017 18:15 Pandya, Akash wrote: > Hi all, > > I have ran a simulation with a protein and multiple ligand molecules > inserted randomly inside a box. I w

[gmx-users] Protein-ligand binding Cut-offs

Hi all, I have ran a simulation with a protein and multiple ligand molecules inserted randomly inside a box. I want to isolate those ligand molecules that are closest to the protein by a cut-off of four angstroms or so. Is there a command I could use to do this for me or would I have to use a m

Re: [gmx-users] Protein-Ligand

On 5/16/17 1:31 PM, RAHUL SURESH wrote: Dear Justin Thank you much. About the term "curved", even am not exactly clear about it. Book by prof Pamela states that sentence. As I feel she must be explaining about much deformed protein. Well, that's too many unknowns. If you're worried about a

Re: [gmx-users] Protein-Ligand

Dear Justin Thank you much. About the term "curved", even am not exactly clear about it. Book by prof Pamela states that sentence. As I feel she must be explaining about much deformed protein. On Tue, 16 May 2017 at 7:41 PM, Justin Lemkul wrote: > > > On 5/15/17 9:12 AM, RAHUL SURESH wrote: >

Re: [gmx-users] Protein-Ligand

On 5/15/17 9:12 AM, RAHUL SURESH wrote: Dear Users I am tryjng to simulate protein ligand complex using charmm36ff for 100ns. I found the ligand moving away from the protein around 55ns. I don't think it s a pbc effect. Is there anything I have done wrong or Should I add any additional command

[gmx-users] Protein-Ligand

Dear Users I am tryjng to simulate protein ligand complex using charmm36ff for 100ns. I found the ligand moving away from the protein around 55ns. I don't think it s a pbc effect. Is there anything I have done wrong or Should I add any additional commands.? Await your valuable advice. PS: Will th

Re: [gmx-users] protein ligand complex Energy Minimisation

Hi, On Fri, May 5, 2017 at 1:44 PM Patel, Hershna wrote: > > Dear Gromacs users > > > I am trying to do energy minimisation of a protein-ligand complex. When > visualising the output trajectory and .gro file, the structure of the > ligand becomes distorted. The same thing happens when constraini

Re: [gmx-users] protein ligand complex Energy Minimisation

HI, It will be very helpful if you can provide the log file and I think this is a note by gromacs and not a warning. -- 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.or

[gmx-users] protein ligand complex Energy Minimisation

Dear Gromacs users I am trying to do energy minimisation of a protein-ligand complex. When visualising the output trajectory and .gro file, the structure of the ligand becomes distorted. The same thing happens when constraining all-bonds during EM. After running grompp, there is this note:

Re: [gmx-users] protein-ligand simmulation

now it is working my further concern is to put my ligand in its native location and then simulate so can you please tell me how to simulate ligand in a particular site of protein.? On Wed, Apr 26, 2017 at 7:46 PM, Justin Lemkul wrote: > > > On 4/26/17 9:22 AM, Aman Deep wrote: > >> I am trying t

Re: [gmx-users] protein-ligand simmulation

On 4/26/17 9:22 AM, Aman Deep wrote: I am trying to simulate protein-ligand complex simulation and I have followed the tutorial of Bevan lab but in energy minimization step it gives me this error... *Fatal error:* *Atom type CH1 not found* *For more information and tips for troubleshooting, pl

[gmx-users] protein-ligand simmulation

I am trying to simulate protein-ligand complex simulation and I have followed the tutorial of Bevan lab but in energy minimization step it gives me this error... *Fatal error:* *Atom type CH1 not found* *For more information and tips for troubleshooting, please check the GROMACS* I have made drug

Re: [gmx-users] Protein-ligand

Thank you Justin On Wed, Apr 19, 2017 at 6:23 PM, Justin Lemkul wrote: > > > On 4/19/17 8:40 AM, RAHUL SURESH wrote: > >> Dear Justin, >> Thank you >> >> But What do you mean my appropriate energygrps.? Protein ligand.? Will >> that >> give interaction energy between ligand and protein.? >> > >

Re: [gmx-users] Protein-ligand

On 4/19/17 8:40 AM, RAHUL SURESH wrote: Dear Justin, Thank you But What do you mean my appropriate energygrps.? Protein ligand.? Will that give interaction energy between ligand and protein.? Yes. -Justin On Wed, 19 Apr 2017 at 5:17 PM, Justin Lemkul wrote: On 4/19/17 6:50 AM, RAHUL

Re: [gmx-users] Protein-ligand

Dear Justin, Thank you But What do you mean my appropriate energygrps.? Protein ligand.? Will that give interaction energy between ligand and protein.? On Wed, 19 Apr 2017 at 5:17 PM, Justin Lemkul wrote: > > > On 4/19/17 6:50 AM, RAHUL SURESH wrote: > > Dear Gromacs users > > > > how to determi

Re: [gmx-users] Protein-ligand

On 4/19/17 6:50 AM, RAHUL SURESH wrote: Dear Gromacs users how to determine the interaction energy between ligand and protein at each frame of simulation? Set appropriate energygrps in the .mdp file, create a new .tpr and use mdrun -rerun to recalculate the interaction energies from the ex

[gmx-users] Protein-ligand

Dear Gromacs users how to determine the interaction energy between ligand and protein at each frame of simulation? -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/M

Re: [gmx-users] Protein ligand complex simulation

Hi, Look at your docking result before you use it for something else. (Same goes for any computed result from any software.) Mark On Mon, 3 Apr 2017 14:06 RAHUL SURESH wrote: > The ligand is out of protein in the very first frame of production run. > Then that should be my docking error.? > >

Re: [gmx-users] Protein ligand complex simulation

On 4/3/17 8:05 AM, RAHUL SURESH wrote: The ligand is out of protein in the very first frame of production run. Then that should be my docking error.? It sounds like your starting configuration was prepared incorrectly (however you manipulated it to prepare the system) or this is a PBC effe

Re: [gmx-users] Protein ligand complex simulation

The ligand is out of protein in the very first frame of production run. Then that should be my docking error.? On Mon, 3 Apr 2017 at 5:30 PM, Justin Lemkul wrote: > > > On 4/3/17 7:56 AM, RAHUL SURESH wrote: > > Dear Justin > > > > First I apologise for the error I had made in my previous mail.

Re: [gmx-users] Protein ligand complex simulation

On 4/3/17 7:56 AM, RAHUL SURESH wrote: Dear Justin First I apologise for the error I had made in my previous mail. It's during production. I have recentered it. The ligand is out of the protein. The ligand is not in position where I docked. Then watch the recentered trajectory to see what

Re: [gmx-users] Protein ligand complex simulation

Dear Justin First I apologise for the error I had made in my previous mail. It's during production. I have recentered it. The ligand is out of the protein. The ligand is not in position where I docked. On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul wrote: > > > On 4/1/17 8:59 AM, RAHUL SURESH w

Re: [gmx-users] Protein ligand complex simulation

On 4/1/17 8:59 AM, RAHUL SURESH wrote: I followed the complex simulation tutorial. Minimisation for 2ns FYI there is no time during energy minimization, so you did not do "2 ns" of minimization. I used auto dock to dock ligand with protein. During simulation I find the ligand out of prot

Re: [gmx-users] Protein ligand complex simulation

I mean the ligand is not bonded with the protein. On Sat, 1 Apr 2017 at 6:29 PM, RAHUL SURESH wrote: > I followed the complex simulation tutorial. Minimisation for 2ns > > I used auto dock to dock ligand with protein. During simulation I find the > ligand out of protein. Is that usual? > -- > *

[gmx-users] Protein ligand complex simulation

I followed the complex simulation tutorial. Minimisation for 2ns I used auto dock to dock ligand with protein. During simulation I find the ligand out of protein. Is that usual? -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list *

Re: [gmx-users] protein-ligand

Yeah. Thank you Mr.Justin On Tue, Mar 28, 2017 at 7:43 PM, Justin Lemkul wrote: > > > On 3/28/17 10:06 AM, RAHUL SURESH wrote: > >> But in case of charmm36ff, the script file will not generate .gro file for >> ligand I believe. In that case how will i generate gro file? >> >> > I responded to y

Re: [gmx-users] protein-ligand

On 3/28/17 10:06 AM, RAHUL SURESH wrote: But in case of charmm36ff, the script file will not generate .gro file for ligand I believe. In that case how will i generate gro file? I responded to your exact same question yesterday. Please read that. -Justin On Tue, Mar 28, 2017 at 5:28 PM,

Re: [gmx-users] protein-ligand

But in case of charmm36ff, the script file will not generate .gro file for ligand I believe. In that case how will i generate gro file? On Tue, Mar 28, 2017 at 5:28 PM, Justin Lemkul wrote: > > > On 3/27/17 11:49 PM, RAHUL SURESH wrote: > >> How will I add ligand .gro file in protein .gro file

Re: [gmx-users] protein-ligand

On 3/27/17 11:49 PM, RAHUL SURESH wrote: How will I add ligand .gro file in protein .gro file to make a complex .? With a text editor. Go through my tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html -Justin On Tue, 28 Mar 2017 at 2:12 AM

Re: [gmx-users] protein-ligand

How will I add ligand .gro file in protein .gro file to make a complex .? On Tue, 28 Mar 2017 at 2:12 AM, Justin Lemkul wrote: > > > On 3/27/17 4:02 PM, RAHUL SURESH wrote: > > In protein-ligand simulation using charmm36ff, how to generate gro file > for > > ligand to add it to the protein gro fi

Re: [gmx-users] protein-ligand

On 3/27/17 4:02 PM, RAHUL SURESH wrote: In protein-ligand simulation using charmm36ff, how to generate gro file for ligand to add it to the protein gro file? You don't strictly need a .gro file, since GROMACS can handle PDB and other formats, but in short, you can convert between formats ea

[gmx-users] protein-ligand

In protein-ligand simulation using charmm36ff, how to generate gro file for ligand to add it to the protein gro file? -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] protein-ligand complex mdrun errors

On 3/17/17 12:43 PM, Vignesh Waran wrote: respected sir, i am using protein-ligand complex tutorials .this my problem .i have all process has been done but like energy minimization result is not coming what we do sir ? my command line gmx mdrun -v -deffnm em how to find the clarify the

[gmx-users] protein-ligand complex mdrun errors

espected sir, i am using protein-ligand complex tutorials .this my problem .i have all process has been done but like energy minimization result is not coming what we do sir ? my command line gmx mdrun -v -deffnm em how to find the clarify the problem? pls tell me sir GROMACS: gmx m

[gmx-users] protein-ligand complex mdrun errors

espected sir, i am using protein-ligand complex tutorials .this my problem .i have all process has been done but like energy minimization result is not coming what we do sir ? my command line gmx mdrun -v -deffnm em how to find the clarify the problem? pls tell me sir GROMACS: gmx m

[gmx-users] protein-ligand complex mdrun errors

respected sir, i am using protein-ligand complex tutorials .this my problem .i have all process has been done but like energy minimization result is not coming what we do sir ? my command line gmx mdrun -v -deffnm em how to find the clarify the problem? pls tell me sir GROMACS: gmx

Re: [gmx-users] Protein-ligand opls ff

On 2/24/17 1:12 AM, Chetan Puri wrote: I want to use Desmond out.cms file for gromacs, as I want to compare MD output from Desmond and gromacs . Since Desmond uses OPLS, I will also be needing OPLS in Gromacs If you previously ran the simulation in another program, presumably you have all th

Re: [gmx-users] Protein-ligand opls ff

I want to use Desmond out.cms file for gromacs, as I want to compare MD output from Desmond and gromacs . Since Desmond uses OPLS, I will also be needing OPLS in Gromacs On 24 Feb 2017 12:11 am, "Justin Lemkul" wrote: > > > On 2/23/17 10:53 AM, Chetan Puri wrote: > >> I have few questions >> 1) I

Re: [gmx-users] Protein-ligand opls ff

force fields). Cheers Tom From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 23 February 2017 18:40 To: gmx-us...@gromacs.org Subject: Re: [gmx-users

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