Re: [gmx-users] Regarding creating the molecules...

Here is the link to the GROMACS page was referring to http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation On 14 Jun 2017 3:40 PM, "Dallas Warren" wrote: > Please keep discussion to the emailing list. > > 1/ and 2/ to construct the coordinate

Re: [gmx-users] Regarding creating the molecules...

Please keep discussion to the emailing list. 1/ and 2/ to construct the coordinate file for the molecules, I personally use Sybyl or the ATB website, but I'm sure there are many more options out there. GROMACS website may have links to some as well. 3/ not entirely sure what you are asking

Re: [gmx-users] Ion flux/current

Hi, It would be helpful for us (user's of Gromacs and people who do MD) to get a predefined code for a particular reason. Kindly share it, or you can provide it with your work so that we can cite your paper too. Thanks -- Gromacs Users mailing list * Please search the archive at

[gmx-users] using groups in index for gmx select

Hi gmx users, Can anyone please tell me how to use a group in index file in gmx select. For example - *gmx select -n index.ndx -select 'name "OH2" and within 2 of com of name "P and r 1-36"' -on P-water.ndx -s step7_production.tpr* does not write out anything in the index (P-water.ndx) file. I

[gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

Hi I have read the chapter 5 of manual but i am confuse how can i add residue into heme atom of .rtp ff this is the coordinate due to which error come HETATM 1529 O01 HEM 187 3.996 19.101 70.594 0.00 0.00 O kindly guide me how i can make changes in the rtp file and .atp so

Re: [gmx-users] defining two interactions potentials for same pair of atoms

Thanks for the reply Mark. On Wed, Jun 14, 2017 at 4:34 AM, Mark Abraham wrote: > Hi, > > On Tue, Jun 13, 2017 at 3:26 PM Sahithya S Iyer wrote: > > > Hi gmx users, > > > > Can someone please tell me if it is possible to use two user defined > >

Re: [gmx-users] how to select index group in gmx hbond or any other command

On 6/13/17 9:02 PM, Md. Imrul Reza Shishir wrote: Dear all I have to run gmx hbond command for several time. So i want to know is there any command for gmx hbond like gmx distance (-select) to select specific index group for analysis gmx hbond. gmx hbond -f *.xtc -s *.tpr -n *.ndx -num *.xvg

[gmx-users] how to select index group in gmx hbond or any other command

Dear all I have to run gmx hbond command for several time. So i want to know is there any command for gmx hbond like gmx distance (-select) to select specific index group for analysis gmx hbond. gmx hbond -f *.xtc -s *.tpr -n *.ndx -num *.xvg for this command, I want to select different index

Re: [gmx-users] ATB topology: itp to top conversion

Thank you Mark and Justin! That makes sense, of course!!! Many thanks. With best wishes Anna > On Jun 13, 2017, at 17:22, Mark Abraham wrote: > > Hi, > >> On Wed, Jun 14, 2017 at 1:07 AM Anna Lappala wrote: >> >> Dear all, >> >> I am

Re: [gmx-users] Doubt about Free Energy control Minimization

On 6/13/17 4:31 PM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, I aspire to derive energy-minimum structures when the interaction potential energy between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, 0.1. I presume the following Free Energy minimization code

Re: [gmx-users] ATB topology: itp to top conversion

Hi, On Wed, Jun 14, 2017 at 1:07 AM Anna Lappala wrote: > Dear all, > > I am confused: I have my pdb file as well as the itp file produced by ATB. > I want to convert these into top and gro files but the molecule is not > recognised by the forcefield when I do the

Re: [gmx-users] ATB topology: itp to top conversion

On 6/13/17 7:06 PM, Anna Lappala wrote: Dear all, I am confused: I have my pdb file as well as the itp file produced by ATB. I want to convert these into top and gro files but the molecule is not recognised by the forcefield when I do the following: pdb2gmx -f input.pdb -o output.gro -i

Re: [gmx-users] Fwd: Using amber-ff14SB forcefield port to GROMACS - blowing up error

Hi, On Mon, Jun 12, 2017 at 7:14 PM p.kartheek wrote: > Dear experts, > Currently I am trying to model Protein-DNA complex systems, with updated > Amber forcefield parameters. Parmbsc1 for DNA and *ff14SB* for protein, > considering the unavailability of theses updated

[gmx-users] ATB topology: itp to top conversion

Dear all, I am confused: I have my pdb file as well as the itp file produced by ATB. I want to convert these into top and gro files but the molecule is not recognised by the forcefield when I do the following: pdb2gmx -f input.pdb -o output.gro -i topology.itp I have looked through tutorials

Re: [gmx-users] defining two interactions potentials for same pair of atoms

Hi, On Tue, Jun 13, 2017 at 3:26 PM Sahithya S Iyer wrote: > Hi gmx users, > > Can someone please tell me if it is possible to use two user defined > (non-bonded) potentials for the same pair of interaction sites. > For instance, if I have beads A and B, I can define non

Re: [gmx-users] WARNING: WARNING: Residue 1 named MET 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 angle in that entry

Hi, On Tue, Jun 13, 2017 at 11:10 PM Rana Rehan Khalid wrote: > dear sir > > I remove the hydrogen from my protein before creating the .top file rather > then use ignore hydrogen command kindly tell me is it right to remove the > hydrogen before simulation next gromacs steps

Re: [gmx-users] Fatal error: Atom N01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

Hi, Please do not use all capital letters in emails. People think it is like shouting. On Tue, Jun 13, 2017 at 11:25 PM Rana Rehan Khalid wrote: > SIR > > I AM FACING ABOVE PROBLEM CAN YOU GUIDE ME HOW CAN I MAKE CHANGES IN .RTP > FILE TO ADD THAT KIND OF INTERACTION

Re: [gmx-users] Regarding the forcefield, topology..

1 and 2 are for you to research and decide. Do a literature search for simulation of those molecules, see what others have done etc. Re 3) http://www.gromacs.org/Documentation/Terminology/Force_Fields#Usage Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of

[gmx-users] Ion flux/current

Hi all, This isn't a question. My boss wrote a very nice utility that calculates ionic fluxes (yes, my boss writes utilities for me). It is a neat perl script that accepts a trajectory in pdb format and spits out ion fluxes for all ion types selected by the user. We may add a few other useful

[gmx-users] Fatal error: Atom N01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

SIR I AM FACING ABOVE PROBLEM CAN YOU GUIDE ME HOW CAN I MAKE CHANGES IN .RTP FILE TO ADD THAT KIND OF INTERACTION BETWEEN FE AND NITRIC OXIDE NO -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] WARNING: WARNING: Residue 1 named MET 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 angle in that entry

dear sir I remove the hydrogen from my protein before creating the .top file rather then use ignore hydrogen command kindly tell me is it right to remove the hydrogen before simulation next gromacs steps -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Doubt about Free Energy control Minimization

Dear Justin, I aspire to derive energy-minimum structures when the interaction potential energy between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, 0.1. I presume the following Free Energy minimization code mentioned in gromacs tutorial may do the trick. I would

Re: [gmx-users] Pulling COM option

I have already used enforced rotation to move gamma and yes it works good but now I want to just pull gamma a certain direction just by pulling it and see how the system reacts to this kind of force. I want to understand if it is possible to do this with the pulling COM option of GROMACS and

[gmx-users] How to find the loading capacity of a nanostructure?

Dear all, I have performed 50 ns of production MD simulation on a polymer that contains several drug molecules. Now I need to find how many drugs (and which ones) remain encapsulated into the polymer. I measured the COM separation distance between polymer and each drug. However, the problem is

[gmx-users] How to find the loading capacity of a nanostructure?

Dear all, I have performed 50 ns of production MD simulation on a polymer that contains several drug molecules. Now I need to find how many drugs (and which ones) remain encapsulated into the polymer. I measured the COM separation distance between polymer and each drug. However, the problem is

Re: [gmx-users] Pulling COM option

On 6/13/17 1:58 PM, Angela Marcela Murcia Rios wrote: Hi Justin, I don't want two opposing forces acting on gamma and I don't want to apply it to all of gamma only a specific region, which is what enforced rotation will do. I only want to apply one directional force onto one side of gamma

Re: [gmx-users] Pulling COM option

Hi Justin, I don't want two opposing forces acting on gamma and I don't want to apply it to all of gamma only a specific region, which is what enforced rotation will do. I only want to apply one directional force onto one side of gamma and see how the whole system behaves. But the problem I'm

Re: [gmx-users] Doubt about g_lie

On 6/13/17 9:02 AM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, I have used PME in the production runs of my systems for finding Delta G_Binding using g_lie. But many threads on Gromacs forum warn against it and advise to rerun the whole trajectory using Reaction field Zero, but the

Re: [gmx-users] How to interpret gmx H_bond analysis?

On 6/13/17 11:25 AM, Adarsh V. K. wrote: Dear gmx users, How to interpret gmx H_bond analysis? I have done 20 ns simulation of a protein-ligand complex (Enzyme-inhibitor). The H-bond analysis shows absence of H-bonds (zero) in several frames during the first 2ns of simulation. But from 2 ns

Re: [gmx-users] Pulling COM option

On 6/13/17 1:48 PM, Angela Marcela Murcia Rios wrote: Hi, I'm not really intersected in the information that the Pulling COM option provides. I am really just interested in getting my protein move in a specific direction until it completes a full circle. To be more specific my system is

Re: [gmx-users] Pulling COM option

Hi, I'm not really intersected in the information that the Pulling COM option provides. I am really just interested in getting my protein move in a specific direction until it completes a full circle. To be more specific my system is F1 ATPase and I just want to pull the gamma subunit until

Re: [gmx-users] Pulling COM option

Hi, Out of curiosity, i wanted to ask you what information you will get by rotating protein by 360 degrees.? -- 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

[gmx-users] How to interpret gmx H_bond analysis?

Dear gmx users, How to interpret gmx H_bond analysis? I have done 20 ns simulation of a protein-ligand complex (Enzyme-inhibitor). The H-bond analysis shows absence of H-bonds (zero) in several frames during the first 2ns of simulation. But from 2 ns onwards consistent (at least one) H bonds are

[gmx-users] How to interpret gmx H_bond analysis?

Dear gmx users, How to interpret gmx H_bond analysis? I have done 20 ns simulation of a protein-ligand complex (Enzyme-inhibitor). The H-bond analysis shows absence of H-bonds (zero) in several frames during the first 2ns of simulation. But from 2 ns onwards consistent (at least one) H bonds are

[gmx-users] defining two interactions potentials for same pair of atoms

Hi gmx users, Can someone please tell me if it is possible to use two user defined (non-bonded) potentials for the same pair of interaction sites. For instance, if I have beads A and B, I can define non bonded interactions as table_A_A.xvg, table_A_B.xvg, and table_B_B.xvgfor these two sites. But

[gmx-users] Doubt about g_lie

Dear Justin, I have used PME in the production runs of my systems for finding Delta G_Binding using g_lie. But many threads on Gromacs forum warn against it and advise to rerun the whole trajectory using Reaction field Zero, but the cutoff for this rerun is not clearly given. Some threads say

Re: [gmx-users] error in running md

On 6/13/17 8:51 AM, VARSHA RANI wrote: Thanks for reply. As suggested by Mark Abraham, I ran same calculation for energy minimization for pentacene single molecule. minim.mdp is same and screen output is writing lowest energy coordinates. Steepest Descents converged to Fmax < 10 in 78 steps

Re: [gmx-users] error in running md

Thanks for reply. As suggested by Mark Abraham, I ran same calculation for energy minimization for pentacene single molecule. minim.mdp is same and screen output is writing lowest energy coordinates. Steepest Descents converged to Fmax < 10 in 78 steps Potential Energy = 1.0244328e+02 Maximum

Re: [gmx-users] Regarding hydrogen bond dynamics

On 6/13/17 2:44 AM, Dilip H N wrote: Hello, I want to study the hydrogen bond dynamics (continuous and intermittent) of my system of amino acid with solvent mixture. I have tried gmx hbond..but i am unable to figure it out Is there any other means to study the hydrogen bonding of the above

Re: [gmx-users] Periodic Cell of Cyclohexane--LINCS Warnings

On 6/13/17 12:13 AM, Billy Williams-Noonan wrote: "Side issue, not related to your problem - use gmx grompp -t state.cpt to get the full-precision coordinates and box." I used gmx energy to plot the box coordinates over time. Using P-R with a 2 fs timestep and tau_p of 2 ps, the box shrinks

Re: [gmx-users] Technqiues for Applying Assymmetric Ion Concentrations?

On 6/12/17 10:47 PM, petar.zuvela wrote: Isn't it just easier to compute the number of ions ? It is basic chem and quite simple. N (atoms) = n / mol * Na / mol -1 n / mol = c / mol dm-3 * V / dm3 Here V is volume of the box, and c is concentration of either of the ions. After computing the

Re: [gmx-users] Doubt about Free Energy Calculations using g_bar

On 6/12/17 5:44 PM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, So if I am interpreting it correct, it is reasonable if sc-coul = no even when partial coulomb interpolation takes place during transition from couple-lambda0 = none to couple-lambda1 = vdw-q , right? Yes. But again I

Re: [gmx-users] GPCR insertion in POPC_Cholesterol bilayer

Thanks for the reply. I have built the bilayer using CHARMM- gui. On Jun 13, 2017 2:20 AM, "Justin Lemkul" wrote: On 6/12/17 4:12 PM, Archana Sonawani-Jagtap wrote: > Hi all, > > I am trying to insert GPCR in POPC with 30 mol% cholesterol bilayer. I am > using Inflategro

Re: [gmx-users] error in running md

Hi, Technically this is energy minimization, not md. But likely the energy should be negative. It's hard to help because you haven't told us what is in the system, but if it's multiple organic molecules, start with one, to see if your topology works appropriately. Mark On Tue, 13 Jun 2017 12:45

Re: [gmx-users] error in running md

Check structure, mainly atom numbers given in messages. Bad contacts or something. On Tuesday, June 13, 2017 1:45 PM, VARSHA RANI wrote: Hi, I ran minim.mdp for my system with 3456 atoms.  But lowest energy after minimization is positive. *here is th screen

[gmx-users] error in running md

Hi, I ran minim.mdp for my system with 3456 atoms. But lowest energy after minimization is positive. *here is th screen output* Step= 4509, Dmax= 4.5e-05 nm, Epot= 4.06554e+02 Fmax= 9.86206e+00, atom= 3521 writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.1#

[gmx-users] Regarding hydrogen bond dynamics

Hello, I want to study the hydrogen bond dynamics (continuous and intermittent) of my system of amino acid with solvent mixture. I have tried gmx hbond..but i am unable to figure it out Is there any other means to study the hydrogen bonding of the above system Thank you. -- With Best

[gmx-users] Regarding hydrogen bond dynamics

Hello, I want to study the hydrogen bond dynamics (continuous and intermittent) of my system of amino acid with solvent mixture. I have tried gmx hbond..but i am unable to figure it out Is there any other means to study the hydrogen bonding of the above system Thank you. -- With Best