[gmx-users] Free energy calculation and Lincs warning

Dear Gromacs users I am doing free energy calculation of the protein-ligand system in gromacs 2020 in which I am annihilating ligand by removing charges and vdw interactions. During Vdw removal I am facing lincs warning and my system crashes by generating different pdb structures. I have tried to

Re: [gmx-users] Warning: Short Bond pdb2gmx (Justin Lemkul) (Sadaf Rani)

Thank you very much, Justin, for your valuable feedback. Regards. Sadaf -- 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

Re: [gmx-users] Lincs warning in free energy calculation (FAISAL NABI)

Dear Gromacs users I am using amber99sb-ildn.ff force field for protein and I used GAFF for ligand parameterization. I tried different options e.g using constraint =all bonds as well as h-bonds. Reducing the time step to 1 fs but still, I could not solve the problem and get lincs warning production

Re: [gmx-users] Warning: Short Bond pdb2gmx (Justin Lemkul)

Dear Justin I want to get the equilibrium value for bond, angle and dihedral restraints to use in free energy calculation as mentioned in:- https://pubs.acs.org/doi/abs/10.1021/jacs.6b11467 Looking forward to your kind suggestions, please. Thanks. Sadaf -- Gromacs Users mailing list * Please s

[gmx-users] Warning: Short Bond pdb2gmx

Dear Gromacs users I did 50ns MD simulation of a protein-ligand complex. From this trajectory, I extracted region of trajectory having stable rmsd and generated an average structure. I want to run this average structure to get an idea of setting some restraints. but when I do gmx pdb2gmx I get foll

Re: [gmx-users] Invalid atomtype format (Justin Lemkul

Dear Justin I have removed the blank lines but getting a new warning while doing gmx pdb2gmx:- WARNING: Duplicate line found in or between hackblock and rtp entries I am not getting what else is wrong. Could you please help me to figure out. I have shared the file on the following link:- https:/

Re: [gmx-users] Invalid atomtype format (Justin Lemkul)

Dear Justin I have shared the files for the users mailing list on the following link. https://www.dropbox.com/s/bfaq8z8iqojdm0r/Atom_type_error%20files.zip?dl=0 Thanks and Regards. Sadaf -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/

[gmx-users] Invalid atomtype format

Dear Gromacs users I am facing a problem between different versions of gromacs for gmx pdb2gmx. I have a protein-ligand system, I did all the necessary steps mentioned in gromacs manual for adding new residue to force field. When I run this in gromacs 2019 it gives me a warning as below:- Fatal err

[gmx-users] Error in pdb2gmx

Dear Gromacs users I have tried to sort out this problem with gromacs 2020 and 2019 versions. I gromacs 2019, It gives:- All occupancies are one Opening force field file ./amber99sb-ildn.ff/atomtypes.atp Atomtype 106 Invalid format: However, It generates a topology file. In gromacs 2020, it gives:

Re: [gmx-users] error in pdb2gmx

Dear Gromacs users I have tried to sort out this problem with gromacs 2020 and 2019 versions. I gromacs 2019, It gives:- All occupancies are one Opening force field file ./amber99sb-ildn.ff/atomtypes.atp Atomtype 106 Invalid format: However, It generates a topology file. In gromacs 2020, it gives:

[gmx-users] error in pdb2gmx

Dear Gromacs users I am facing a strange problem while doing pdb2gmx:- When I use the command:- gmx pdb2gmx -f 74A-G.pdb -o 74A-G.gro It shows the following:- going to rename ./amber99sb-ildn.ff/aminoacids.r2b Opening force field file ./amber99sb-ildn.ff/aminoacids.r2b going to rename ./amber99sb-

Re: [gmx-users] duplicate angle index- angle restraint

Dear Justin As per table 5.14 in manual, For angle restraints it selects [image: image.png] Also in manual under heading *Angle restraints*, it is mentioned that these are used to restrain the angle between two pairs of particles or between one pair of particles and the 𝑧-axis. Could you please c

[gmx-users] duplicate angle index- angle restraint

Dear Gromacs users I am putting some restraints on bonds angles and dihedrals during free energy calculations for which the topology file section is as below:- ; distance restraints [ bonds ] ;i j type r0A r1A r2AfcAr0B r1B r2B fcB 7968 21310 0.382

Re: [gmx-users] segmentation fault gmx do_dssp

Dear Justin and Qinghua I am using gromacs 2020 for analysis and dssp version on my system is 2.2.1. Which version of dssp would be compatible with gromacs 2020? Qinghua, I am already using the stripped trajectory. Any suggestions would be appreciated. Thanks. Sadaf -- Gromacs Users mailing list

[gmx-users] segmentation fault gmx do_dssp

Dear Gromacs users I am doing an analysis of protein-ligand MD simulation of 150ns. I am trying to calculate secondary structure as below:- gmx do_dssp -f md_noPBC.xtc -s md.tpr -o ss.xpm -tu ns -dt 1 But I am getting segmentation fault error. Reading file md.tpr, VERSION 2020-UNCHECKED (single p

[gmx-users] restarting a simulation

Dear Gromacs users I am restarting a simulation with the following command:- mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append However, I am getting following error message. All the below-named files are there in my directory but it still complains the same. Inconsistency in user input:

[gmx-users] Fwd: no atom pairs for dispersion correction

Dear Gromacs users I am running an MD simulation of the protein-ligand complex. At the start of the production run, I am getting this warning. What does it mean and how should I fix it? *WARNING: There are no atom pairs for dispersion correction* Thanks in advance. Sadaf -- Gromacs Users mailin

[gmx-users] no atom pairs for dispersion correction

Dear Gromacs users I am running an MD simulation of the protein-ligand complex. At the start of the production run, I am getting this warning. What does it mean and how should I fix it? *WARNING: There are no atom pairs for dispersion correction* Thanks in advance. Sadaf -- Gromacs Users mailin

[gmx-users] Lincs warning in free energy calculation

Dear Gromacs users I ran an MD simulation for 3ns and from the last coordinates started a free energy calculation for 3ns. My system is well equilibrated but after 710725 steps I am getting Lincs warning every time as below:- WARNING: There are no atom pairs for dispersion correction starting mdru

Re: [gmx-users] Error in free energy calculation (Chris Neale)

Dear Chris Thank you very much for giving your comprehensive information on my mdp options. In my current simulation, I am trying to switch off coulombic interactions while keeping VDW on. In gromacs manual, it is mentioned that with parallel simulations and/or non-bonded force calculation on the G

[gmx-users] Error in free energy calculation

Dear Gromacs users I am running a free energy calculation, my simulation crashes and generates different PDB structures I have well equilibrated the system before going to the production and the system seems stable. My input file for production run is as below:- ; Run control integrator

[gmx-users] makes sense for Ryckaert Bellemans dihs. only.

Dear Gromacs users I am calculating a dihedral angle between certain atoms by following command:- gmx angle -type dihedral -f md_1000ps.xtc -n dihedral.ndx -ov group.xvg -of trans.xvg Group 0 ( dihedral1) has 4 elements Group 1 ( dihedral2) has 4 elements Group 2 (

[gmx-users] Negative Pressure during equilibration

Dear Gromacs users I am running a free energy test calculation and using position restraints for all of the system. At the end of pressure equilibration I am getting negative average pressure as below:- Energy Average Err.Est. RMSD Tot-Drift ---

Re: [gmx-users] how to generate average structure from trajectory

Dear Subhomoi Thanks for your reply. I was doing the following:- discarding 1 ns trajectory by the following command:- gmx trjconv -f md.xtc -s md.gro -n index.ndx -b 1000 -e 2000 -o md_1000ps.xtc Extracting average structure by the following command:- gmx rmsf -s md.tpr -f md_1000ps.xtc -o rmsf

[gmx-users] how to generate average structure from trajectory

Dear Gromacs users I want to get the average structure of a 10ns simulation by discarding earlier 1ns run. What is the best way to get the average structure? Thanks in advance. Sadaf -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-U

[gmx-users] Fwd: regarding dihedral restraints

Dear Gromacs users I am restraining three dihedral angles between atoms of two different residues. when I measure it using the following command:- gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of trans.xvg I am getting one of my dihedrals graphs as mentioned in the link.

[gmx-users] regarding dihedral restraints

Dear Gromacs users I am restraining three dihedral angles between atoms of two different residues. when I measure it using the following command:- gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of trans.xvg I am getting one of my dihedrals graphs as mentioned in the link.

[gmx-users] Fwd: restraints failure problem

Dear Gromacs users I am posting this problem third time in hope to get some suggestions regarding my problem. I am doing a test calculation in MD simulation between ligand and a protein residue for bond angle and dihedral restraints. I have set them in my topology file as below:- ; distance restra

[gmx-users] How to calculate the dihedral angle as a function of time?

Dear Gromacs users I want to calculate the dihedral angle over the simulation time. I tried following commands:- gmx mk_angndx -s topol.tpr -type dihedral which generates an index file for dihedral angles then running:- gmx angle -f md_prod.trr -n angle.ndx -type dihedral gives following group o

Re: [gmx-users] How to cap a single residue in gromacs (Alessandra Villa) (Justin Lemkul)

Dear Justin, thank you for your reply. I have also tried adding ACE and NME as below but it didn't work. 1ACE HC1 0.000 0.000 0.000 0. 0. 0. 1ACE CT2 0.000 0.000 0.000 0. 0. 0. 1ACE HC3 0.000 0.000 0.000 0. 0

[gmx-users] restraints failure problem

Dear Gromacs users I am doing a test calculation in MD simulation between ligand and a protein residue for bond angle and dihedral restraints. I have set them in my topology file as below:- ; distance restraints [ bonds ] ;ij type r0A r1A r2AfcAr0B r1B r2B

Re: [gmx-users] How to cap a single residue in gromacs (Alessandra Villa)

Thank you, Alessandra, for your reply. I have tried TER in the PDB file but it doesn't work. It requires an N and C terminal for amino acid residue. I have prepared residue in avogadros and used these coordinates. ATOM 1 N PHE A 1 0.000 0.000 0.000 1.00 0.00 N1+ ATOM 2

[gmx-users] Problem in energy minimization and domain decomposition

Dear Gromacs users I am getting the following message while running an energy minimization:- There is no domain decomposition for 32 ranks that is compatible with the given box and a minimum cell size of 1.85723 nm I am not using any distance restraint, and selecting box size by the following com

[gmx-users] How to cap a single residue in gromacs

Dear Gromacs users I am trying to make a system with 1 single amino acid(PHE) and 1 Ligand when I run pdb2gmx it gives me error:- Fatal error: In the chosen force field there is no residue type for 'PHE' as a standalone (starting & ending) residue I added ACE and NME terminals as below in the gro

[gmx-users] How to set restraints in free energy calculation?

where I am doing wrong? I will be really grateful. Thanks. Sadaf Rani P.hD. visiting scholar Lancaster University Uk -- 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.gromac

[gmx-users] How to fix restraints in free energy calculation?

7909 7908 3437 3439 1-167.75 0.00.0-69.050.0 41.840 7909 7908 3437 3433 1-172.77 0.00.0 -172.770.0 41.840 Can anyone please suggest me how should I fix this? or where I am doing wrong? I will be really grateful. Thanks Sadaf Rani P.hD. visiting

Re: [gmx-users] putting step wise constraints in energy minimization

16 14:28:08 2020 How should I set the minimization energy of my system as it crashes after some steps of nvt equilibration? Thanks Sadaf Rani Ph.D. visiting student Lancaster university Uk -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_

[gmx-users] putting step wise constraints in energy minimization

Dear Gromacs users I want to run energy minimization in steps first to remove clashes with ions, second keeping position of heavy atoms fixed and thirdly removing all constraints. How can I set this in mdp file for ions and protein atoms? Thanks Sadaf Rani Ph.D. visiting student Lancaster

[gmx-users] how to apply constraints in energy minimization

different pdb structures. How should I solve this Any suggestions will really be appreciated. Thanks. Sadaf Rani Visiting Ph.D. student Lancaster University Uk -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

[gmx-users] how to fix error: Some of these results violate the Second Law of Thermodynamics

anyone please suggest me what could be wrong during my simulation and how should I fix it? Thank you Sadaf Rani Ph.D. visiting student Lancaster University Uk -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

[gmx-users] Assertion failed: Condition: bX

Dear Gromacs users I am getting following message in my log file during MD simulation:-- --- Program: gmx mdrun, version 2018.1 Source file: src/gromacs/mdlib/minimize.cpp (line 582) Function:void write_em_traj(_IO_FILE *, t_commrec *, gm

[gmx-users] list of missing interactions

Dear Gromacs users I am doing free energy calculation of protein-ligand complex and getting again n again same error:- Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: Dih. Rest. of 3 missing 1 Could anyo

[gmx-users] Fwd:

eps, but did not reach the requested Fmax < 10. Potential Energy = -2.2680185e+06 Maximum force = 6.3521606e+02 on atom 4653 Norm of force = 3.6713926e+00 Should I use double precision for energy minimization? I need your suggestions, please. Thanks Sadaf Rani -- Gromacs Users mailin

[gmx-users] (no subject)

max < 10. Potential Energy = -2.2680185e+06 Maximum force = 6.3521606e+02 on atom 4653 Norm of force = 3.6713926e+00 Should I use double precision for energy minimization? I need your suggestions, please. Thanks Sadaf Rani -- Gromacs Users mailing list * Please search the arch

[gmx-users] Problem of lincs in free energy calculations

initial topology had some issue it should not work for any system. Could you please suggest me how should I fix this error? Thanks Sadaf Rani Ph.D. visiting student Lancaster University United kingdom -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] different number of charges and atoms of ligand in free energy calculation

Dear Gromacs users I am simulating the free energy of binding of a ligand with protein using the dual topology method. I am getting the following message in log file:- *There are 28 atoms and 29 charges for free energy perturbation* I have 27 atoms in ligand plus two Na+ ions, It should give an eq

[gmx-users] how to set vdw_lambdas and coul_lambdas

Dear Gromacs users I am trying to run a free energy calculation of ligand with protein in which I am going to transform electrostatics going from lambda 0 to 1 when vdw interactions and restraints are there, and in the second step transforming vdw interactions while switching off electrostatics. T

[gmx-users] Fwd: A list of missing interactions

Dear Gromacs users I am facing this error during free energy calculation of protein-ligand for which I have applied restrained to some atoms of protein residue and ligand. A list of missing interactions: Restraint Pot. of 1 missing 1 Molecule type 'Protein' the first 10 missing int

[gmx-users] A list of missing interactions

Dear Gromacs users I am facing this error during free energy calculation of protein-ligand for which I have applied restrained to some atoms of protein residue and ligand. A list of missing interactions: Restraint Pot. of 1 missing 1 Molecule type 'Protein' the first 10 missing int

[gmx-users] how to set system for absolute free enegy calculation of ligand in protein

Dear Gromacs users I need your suggestions regarding the calculation of free energy of binding in of ligand protein-ligand complex in setting up the system. I am performing binding free energy calculation following alchemical free energy path. I added a single molecule type in topology for both pro

[gmx-users] restraints

Dear Gromacs users I want to run free energy calculation of a protein-ligand complex by putting distance, angle and dihedral restraints between ligand and protein. Before that, I run 1ns MD (without free energy input) in order to know that my ligand restraints are working well or otherwise. However

[gmx-users] Atom O in residue was not found in rtp entry

Dear Gromacs users I have a ligand in my protein for which I make rtp file and included this in my local copy for force field as mentioned in gromacs manual. Also, I added atom types in ffnonbonded.itp and atomtypes.atp atomtypes.atp added residue under protein in residuetypes.dat But I am getting

Re: [gmx-users] setting distance restraints between atoms belonging to different residues (Alessandra Villa)

Hi Alessandra I used it but top file extension is not supported. Should I give a combined PDB file? I got ligand topology from an external server when I will give combined PDB, it will give an error for not having these residues in the database. Could you please suggest which file should I give?

Re: [gmx-users] setting distance restraints between atoms belonging to different residues (Alessandra Villa)

Thank you, Alessandra, for your reply. I have a confusion here that when I merge the topology I will have to reindex ligand atoms. *e.g *I have ligand topology starting with atom number 1 and bond terms, angles, dihedrals have all the connectivity numbering from 1 to so on. When I will change the

[gmx-users] setting distance restraints between atoms belonging to different residues

Hi gromacs users I want to restraint distance, angles and dihedrals between atoms of two different residues; In my case protein atom and ligand atom. Could anybody suggest me the right way of doing it? I have set topology file of complex as below:- Include forcefield parameters #include "amber99s

[gmx-users] gromacs.org_gmx-users-ow...@maillist.sys.kth.se

Thank you Bratin Kumar Das But I have read in articles to specify three degrees of freedom for ligand restraining ; i.e. during free energy calculation and how about setting lambda values. Could you please clear it a bit more. Thanks Sadaf -- Gromacs Users mailing list * Please search the arch

[gmx-users] How to set restraints for Protein-ligand complex in free energy calculation?

I have a protein having two ligands, for which I want to calculate absolute free energy. Could you please suggest me how should I set restraints for two ligands simultaneously? I am trying to do it the first time, any help would really be appreciated. Thanks in advance. Sadaf -- Gromacs Users ma

[gmx-users] How to set restraints for protein-ligand complex in free energy calculation?

Dear gromacs users, I have a protein having two ligands, for which I want to calculate absolute free energy. Could you please suggest me how should I set restraints for two ligands simultaneously? I am trying to do it the first time, any help would really be appreciated. Thanks in advance. Sadaf