[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 use constraints on all bonds and also reduced time step to 1fs but still getting same problem as below:- Overriding thread affinity set outside gmx mdrun WARNING: There are no atom pairs for dispersion correction starting mdrun 'GROtesk MACabre and Sinister in water' 100 steps, 1000.0 ps. Step 853159, time 853.159 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000569, max 0.041969 (between atoms 3430 and 3439) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3435 3437 38.00.1400 0.1415 0.1400 3437 3438 52.20.1080 0.1068 0.1080 3437 3439 39.00.1400 0.1402 0.1400 Step 853159, time 853.159 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000550, max 0.040414 (between atoms 3430 and 3439) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3435 3437 37.80.1400 0.1415 0.1400 3437 3438 51.90.1080 0.1070 0.1080 3437 3439 38.60.1400 0.1403 0.1400 Step 853160, time 853.16 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000833, max 0.054713 (between atoms 3437 and 3438) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3430 3439 30.50.1457 0.1428 0.1400 Please find the mdp file as below:- ; Run control integrator = sd ; stochastic leap-frog integrator dt = 0.001 nsteps = 100 ; 1 ns comm-mode = Linear; remove center of mass translation nstcomm = 100 ; frequency for center of mass motion removal ; Output control nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy= 5000 nstxout-compressed = 5000 ; Bond parameters continuation= yes ; formerly known as 'unconstrained-start' - useful for exact continuations and reruns constraint_algorithm= lincs ; holonomic constraints constraints = all-bonds ; bonds to H are constrained lincs_iter = 1 ; accuracy of LINCS lincs-order = 6; Highest order in the expansion of the constraint coupling matrix ; Neighborsearching and short-range nonbonded interactions cutoff-scheme= verlet nstlist = 10 ns_type = grid rlist= 1.2 pbc = xyz ; 3-D PBC ; Periodic boundary conditions ; Electrostatics coulombtype = PME rcoulomb = 1.2 pme-order = 6; interpolation order for PME (default is 4) fourierspacing = 0.10 ; grid spacing for FFT ewald-rtol = 1e-6 ; relative strength of the Ewald-shifted direct potential at rcoulomb ewald_geometry = 3d ; Ewald sum is performed in all three dimensions ; van der Waals vdwtype = cutoff vdw-modifier = Potential-shift-Verlet verlet-buffer-tolerance = 0.005 rvdw = 1.2 rvdw-switch = 1.0 DispCorr = EnerPres ; apply long range dispersion corrections for Energy and Pressure ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc-grps = system ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 298.15 ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman pcoupltype = isotropic; uniform scaling of box vectors tau_p = 2.0 ; time constant (ps) ref_p = 1.0 ; reference pressure (bar) compressibility = 4.5e-05 ; isothermal compressibility of water (bar^-1) ; velocities gen_vel = no ; Velocity generation is on (if gen_vel is 'yes', continuation should be 'no') gen_seed = -1 ; Use random seed gen_temp = 298.15 ; Free energy control stuff free_energy = yes init_lambda_state= 17 delta_lambda = 0 calc_lambda_neighbors=-1; only immediate neighboring windows ; Vectors of lambda specified here ; Each combination is an index that is retrieved from init_lambda_state for each simulation vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 coul_lambdas = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 run as below:- Step 106202, time 212.404 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.035343, max 2.112628 (between atoms 3770 and 3773) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3437 3438 90.02.2392 0.1552 0.1080 3770 3771 90.00.1045 0.1696 0.1090 3770 3772 90.02.9369 0.1212 0.1090 3770 3773 90.00.1043 0.3393 0.1090 Wrote pdb files with previous and current coordinates Step 106202, time 212.404 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.035038, max 2.096736 (between atoms 3770 and 3773) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3437 3438 90.02.2392 0.1540 0.1080 3770 3771 90.00.1045 0.1689 0.1090 3770 3772 90.02.9369 0.1198 0.1090 3770 3773 90.00.1043 0.3375 0.1090 I would really appreciate your help in fixing this problem I am facing since long. Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 following warning:- Warning: Short Bond (9-10 = 0.042416 nm) Warning: Short Bond (9-11 = 0.0463433 nm) Warning: Short Bond (9-12 = 0.0452425 nm) Warning: Short Bond (13-14 = 0.0407501 nm) Warning: Short Bond (13-15 = 0.0425715 nm) Warning: Short Bond (13-16 = 0.0421154 nm) Warning: Short Bond (65-66 = 0.0418464 nm) Warning: Short Bond (65-67 = 0.0454554 nm) Warning: Short Bond (65-68 = 0.0438005 nm) Warning: Short Bond (103-105 = 0.0498706 nm) Warning: Short Bond (103-106 = 0.0482166 nm) Warning: Short Bond (161-162 = 0.0384303 nm) Warning: Short Bond (161-163 = 0.0395632 nm) Warning: Short Bond (161-164 = 0.0404804 nm) Warning: Short Bond (178-179 = 0.0379231 nm) Warning: Short Bond (178-180 = 0.0350074 nm) Warning: Short Bond (178-181 = 0.0367544 nm) Warning: Short Bond (195-197 = 0.0491068 nm) Warning: Short Bond (240-241 = 0.0410752 nm) Warning: Short Bond (240-242 = 0.0400188 nm) Warning: Short Bond (240-243 = 0.0389276 nm) Warning: Short Bond (244-245 = 0.0395354 nm) Warning: Short Bond (244-246 = 0.0394185 nm) Warning: Short Bond (244-247 = 0.0411173 nm) Warning: Short Bond (254-255 = 0.0496385 nm) Warning: Short Bond (254-256 = 0.0490917 nm) Warning: Short Bond (254-257 = 0.0487225 nm) Warning: Short Bond (320-321 = 0.0389006 nm) Warning: Short Bond (320-322 = 0.0354672 nm) Warning: Short Bond (320-323 = 0.0318275 nm) Warning: Short Bond (332-333 = 0.044048 nm) Warning: Short Bond (332-334 = 0.0431301 nm) Warning: Short Bond (332-335 = 0.0443143 nm) Warning: Short Bond (339-340 = 0.0436942 nm) Warning: Short Bond (339-341 = 0.044572 nm) Warning: Short Bond (339-342 = 0.0438389 nm) Warning: Short Bond (386-387 = 0.0485982 nm) Warning: Short Bond (386-388 = 0.0493432 nm) Warning: Short Bond (400-401 = 0.0365161 nm) Warning: Short Bond (400-402 = 0.043 nm) Warning: Short Bond (400-403 = 0.038517 nm) Warning: Short Bond (552-553 = 0.0489085 nm) Warning: Short Bond (552-554 = 0.0483887 nm) Warning: Short Bond (552-555 = 0.0498913 nm) Warning: Short Bond (556-557 = 0.0345456 nm) Warning: Short Bond (556-558 = 0.0396005 nm) Warning: Short Bond (556-559 = 0.0370519 nm) Warning: Short Bond (575-576 = 0.0458407 nm) Warning: Short Bond (575-577 = 0.0455252 nm) Warning: Short Bond (575-578 = 0.0448519 nm) Warning: Short Bond (664-665 = 0.0423401 nm) Warning: Short Bond (664-666 = 0.0390075 nm) Warning: Short Bond (664-667 = 0.0406177 nm) Warning: Short Bond (671-672 = 0.0369435 nm) Warning: Short Bond (671-673 = 0.0354056 nm) Warning: Short Bond (671-674 = 0.0373171 nm) Warning: Short Bond (725-726 = 0.0389842 nm) Warning: Short Bond (725-727 = 0.0393952 nm) I understand that the average structure is not necessarily anything physically meaningful but how I assume that it can give the equilibrium values to set the restraints. I need your help to figure out this warning, please. Thanks in advance. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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://www.dropbox.com/s/c6tg9q4i0ara3vu/atomtypes.atp?dl=0 Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 error: Invalid atomtype format: '' But it still generates a gro file and topology. But When I am using gromacs 2020, I get the same message of invalid atomtype format as below:- Reading 78I-T.pdb... WARNING: all CONECT records are ignored Read '', 4083 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. WARNING: Chain identifier 'A' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. There are 2 chains and 0 blocks of water and 492 residues with 4083 atoms chain #res #atoms 1 'A' 489 3971 2 'A' 3112 All occupancies are one Opening force field file ./amber99sb-ildn.ff/atomtypes.atp --- Program: gmx pdb2gmx, version 2020-UNCHECKED Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98) Fatal error: *Invalid atomtype format: ''* I am unable to sort out this problem. I have added the atom types of my molecule as mentioned:- ;[ atomtypes ] ; name bond_type mass chargeptype sigma eps nh 14.01000 0.000 A 3.25000e-1 7.11280e-1 hn 1.00800 0.000 A 1.06908e-1 6.56888e-2 ca 12.01000 0.000 A 3.39967e-1 3.59824e-1 nb 14.01000 0.000 A 3.25000e-1 7.11280e-1 h5 1.00800 0.000 A 2.42146e-1 6.27600e-2 nc 14.01000 0.000 A 3.25000e-1 7.11280e-1 cd 12.01000 0.000 A 3.39967e-1 3.59824e-1 na 14.01000 0.000 A 3.25000e-1 7.11280e-1 c3 12.01000 0.000 A 3.39967e-1 4.57730e-1 h2 1.00800 0.000 A 2.29317e-1 6.56888e-2 os 16.0 0.000 A 3.1e-1 7.11280e-1 h1 1.00800 0.000 A 2.47135e-1 6.56888e-2 p5 30.97000 0.000 A 3.74177e-1 8.36800e-1 o 16.0 0.000 A 2.95992e-1 8.78640e-1 oh 16.0 0.000 A 3.06647e-1 8.80314e-1 ho 1.00800 0.000 A 0.0e+0 0.0e+0 h4 1.00800 0.000 A 2.51055e-1 6.27600e-2 c 12.01000 0.000 A 3.39967e-1 3.59824e-1 n 14.01000 0.000 A 3.25000e-1 7.11280e-1 ha 1.00800 0.000 A 2.59964e-1 6.27600e-2 Could you please help me to sort out this problem. Even when the format is incorrect does it mean that gromacs 2019 is generating a wrong topology? Thanks in advance. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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:- Program: gmx pdb2gmx, version 2020-UNCHECKED Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98) Fatal error: Invalid atomtype format: '' I have modified my atomtypes.atp file as below:- ;[ atomtypes ] ; name mass nh 14.01 dnh 14.01 hn 1.008 dhn 1.008 ca 12.01 dca 12.01 nb 14.01 dnb 14.01 h5 1.008 dh5 1.008 nc 14.01 dnc 14.01 cd 12.01 dcd 12.01 na 14.01 dna 14.01 c3 12.01 dc3 12.01 h2 1.008 dh2 1.008 os 16 dos 16 h1 1.008 dh1 1.008 p5 30.97 dp5 30.97 o 16 do 16 oh 16 doh 16 ho 1.008 dho 1.008 h4 1.008 dh4 1.008 c 12.01 dc 12.01 n 14.01 dn 14.01 ha 1.008 dha 1.008 Atomtype 106 is ha, I cant find any thing wrong with it. Could you please help me to fix this error? Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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:- Program: gmx pdb2gmx, version 2020-UNCHECKED Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98) Fatal error: Invalid atomtype format: '' I have modified my atomtypes.atp file as below:- ;[ atomtypes ] ; name mass nh 14.01 dnh 14.01 hn 1.008 dhn 1.008 ca 12.01 dca 12.01 nb 14.01 dnb 14.01 h5 1.008 dh5 1.008 nc 14.01 dnc 14.01 cd 12.01 dcd 12.01 na 14.01 dna 14.01 c3 12.01 dc3 12.01 h2 1.008 dh2 1.008 os 16 dos 16 h1 1.008 dh1 1.008 p5 30.97 dp5 30.97 o 16 do 16 oh 16 doh 16 ho 1.008 dho 1.008 h4 1.008 dh4 1.008 c 12.01 dc 12.01 n 14.01 dn 14.01 ha 1.008 dha 1.008 Atomtype 106 is ha, I cant find any thing wrong with it. Could you please help me to fix this error? Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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-ildn.ff/dna.r2b Opening force field file ./amber99sb-ildn.ff/dna.r2b going to rename ./amber99sb-ildn.ff/rna.r2b Opening force field file ./amber99sb-ildn.ff/rna.r2b Reading 74A-G.pdb... Read '', 4082 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 2 chains and 0 blocks of water and 492 residues with 4082 atoms chain #res #atoms 1 'A' 489 3970 2 'B' 3112 All occupancies are one Opening force field file ./amber99sb-ildn.ff/atomtypes.atp --- Program: gmx pdb2gmx, version 2020-UNCHECKED Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98) Fatal error: Invalid atomtype format: '' However, when I use without gmx, as below:- pdb2gmx -f 74A-G.pdb -o 74A-G.gro It generates topology file successfully. What's wrong with the format in atomtypes.atp I am unable to understand. Could you please help me to find out? I have added a new residue to my forcefield file as mentioned in gromacs manual. Please correct me where I am wrong, I have added following in atomtypes.atp file:- ;[ atomtypes ] ; name bond_type mass chargeptype sigma eps nh 14.01000 0.000 A 3.25000e-1 7.11280e-1 hn 1.00800 0.000 A 1.06908e-1 6.56888e-2 ca 12.01000 0.000 A 3.39967e-1 3.59824e-1 nb 14.01000 0.000 A 3.25000e-1 7.11280e-1 h5 1.00800 0.000 A 2.42146e-1 6.27600e-2 nc 14.01000 0.000 A 3.25000e-1 7.11280e-1 cd 12.01000 0.000 A 3.39967e-1 3.59824e-1 na 14.01000 0.000 A 3.25000e-1 7.11280e-1 c3 12.01000 0.000 A 3.39967e-1 4.57730e-1 h2 1.00800 0.000 A 2.29317e-1 6.56888e-2 os 16.0 0.000 A 3.1e-1 7.11280e-1 h1 1.00800 0.000 A 2.47135e-1 6.56888e-2 p5 30.97000 0.000 A 3.74177e-1 8.36800e-1 o 16.0 0.000 A 2.95992e-1 8.78640e-1 oh 16.0 0.000 A 3.06647e-1 8.80314e-1 ho 1.00800 0.000 A 0.0e+0 0.0e+0 h4 1.00800 0.000 A 2.51055e-1 6.27600e-2 c 12.01000 0.000 A 3.39967e-1 3.59824e-1 n 14.01000 0.000 A 3.25000e-1 7.11280e-1 ha 1.00800 0.000 A 2.59964e-1 6.27600e-2 Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 푧-axis. Could you please correct me in setting this? Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 0.38210.0 0.00.382 0.382 10.0 4184.000 [ angle_restraints ] ; aiajakal typethA fcAmultA thB fcB multB 7959 7968 213 7968 189.400.01 89.40 41.840 1 213 7968 7922 7968 166.780.01 66.78 41.840 1 [ dihedral_restraints ] ; aiajakal typephiA dphiA fcAphiB dphiB fcB 7959 7968 213 218 1174.860.00.0174.860.0 41.840 7922 7968 213 211 1149.950.00.0149.950.0 41.840 7952 7968 213 211 1167.760.00.0167.760.0 41.840 grompp gives me warning that I have duplicate angle index when I remove column 4 (al) in angle restraints I get following message:- ERROR 1 [file topol.top, line 76867]: Incorrect number of parameters - found 5, expected 3 or 6 for Angle Rest. (after the function type). Could you please correct me in fixing this section, I followed table 5.14 of gromacs manual. Thanks in advance for your kind help. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 * 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 precision) Reading file md.tpr, VERSION 2020-UNCHECKED (single precision) Not all residues were recognized (489 from 40652), the result may be inaccurate! Group 0 ( System) has 128526 elements Group 1 (Protein) has 7893 elements Group 2 ( Protein-H) has 3971 elements Group 3 (C-alpha) has 489 elements Group 4 ( Backbone) has 1467 elements Group 5 ( MainChain) has 1957 elements Group 6 ( MainChain+Cb) has 2415 elements Group 7 (MainChain+H) has 2424 elements Group 8 ( SideChain) has 5469 elements Group 9 (SideChain-H) has 2014 elements Group10 (Prot-Masses) has 7893 elements Group11 (non-Protein) has 120633 elements Group12 ( Other) has 173 elements Group13 (G6P) has27 elements Group14 (NAP) has73 elements Group15 (NAS) has73 elements Group16 ( NA) has10 elements Group17 ( Water) has 120450 elements Group18 (SOL) has 120450 elements Group19 ( non-Water) has 8076 elements Group20 (Ion) has10 elements Group21 (G6P) has27 elements Group22 (NAP) has73 elements Group23 (NAS) has73 elements Group24 ( NA) has10 elements Group25 ( Water_and_ions) has 120460 elements Select a group: 5 Selected 5: 'MainChain' There are 489 residues in your selected group dssp cmd='/usr/local/bin/dssp -i ddvbUtB6 2>/dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddvbUtB6 to ./#ddvbUtB6.1# Segmentation fault (core dumped) How should I fix it. As my system is protein-ligand should I choose a group having protein and ligand together for this analysis? Any suggestions will really help. Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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: Some output files listed in the checkpoint file md10_prev.cpt are not present or not named as the output files by the current program:)Expected output files that are present: Expected output files that are not present or named differently: md10.log md10.xtc md10.trr md10.edr md10.xvg To keep your simulation files safe, this simulation will not restart. Either name your output files exactly the same as the previous simulation part (e.g. with -deffnm), or make sure all the output files are present (e.g. run from the same directory as the previous simulation part), or instruct mdrun to write new output files with mdrun -noappend. In the last case, you will not be able to use appending in future for this simulation. I also tried without -append option. Please correct me if I am wrong somewhere. Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 mdrun 'GROtesk MACabre and Sinister in water' 150 steps, 3000.0 ps. Step 710726, time 1421.45 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.03, max 0.23 (between atoms 5470 and 5472) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3437 3438 43.80.1080 0.1080 0.1080 Step 710726, time 1421.45 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.03, max 0.21 (between atoms 5470 and 5472) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3437 3438 43.10.1080 0.1080 0.1080 I have added restraints between atoms of ligand and protein and getting Lincs warning between 1 atom included in restraints as below:- [ bonds ] ;i j type r0A r1A r2AfcAr0B r1B r2B fcB *3437* 790810 0.418 0.418 10.0 0.00.418 0.418 10.0 41840.00 [ angle_restraints ] ; aiajakal typethA fcAmultA thB fcB multB 3437 7908 7906 7908 1100.29 0.01 100.29 418.40 1 7908 3437 3439 *3437* 1146.50 0.01 146.50 418.40 1 [ dihedral_restraints ] ; aiajakal typephiA dphiA fcAphiB dphiB fcB 7906 7908 *3437* 3439 1156.16 0.00.0156.160.0 418.40 7907 7906 7908 *3437* 1-56.93 0.00.0-56.930.0 418.40 7909 *3437* 3430 3435 1131.32 0.00.0131.32 0.0 418.40 Can anyone please suggest to me how Should I fix this error? Any help will be really appreciated. Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 GPU, a value of 20 or 40 often gives the best performance so I chose nstlist as 20. however, I am not very much sure about the best value. Simulations from lambda window 11 to 20 complete very well without any lincs warning. I am getting following performance with the current selection of mdp:- Core t (s) Wall t (s)(%) Time: 630938.07939433.648 1600.0 10h57:13 (ns/day)(hour/ns) Performance:6.5733.651 Finished mdrun on rank 0 Mon Mar 23 07:41:56 2020 I am running simulations from Lambda 0-1 in 21 different windows. For Lambda 9 I am getting the following error:- Step Time 110 2200.0 Energies (kJ/mol) Bond Restraint Pot. AngleProper Dih. Improper Dih. 6.18949e+032.44298e+001.68046e+042.06705e+049.49832e+02 LJ-14 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) 7.91681e+037.10046e+042.30248e+050.0e+00 -2.05702e+06 Coul. recip.Angle Rest. Dih. Rest. PotentialKinetic En. 8.96080e+037.31848e-017.99950e-01 -1.69427e+063.28779e+05 Total EnergyTemperature Pres. DC (bar) Pressure (bar) dVcoul/dl -1.36549e+063.00055e+02 -0.0e+00 -1.54667e+012.05257e+03 dVvdw/dl dVrestraint/dl Constr. rmsd -3.75472e+023.97478e+003.30377e-06 --- Program: gmx mdrun, version 2020-UNCHECKED Source file: src/gromacs/ewald/pme_redistribute.cpp (line 304) MPI rank:5 (out of 16) Fatal error: 2 particles communicated to PME rank 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I have equilibrated the system well and pressure is as below:- Energy Average Err.Est. RMSD Tot-Drift --- Pressure1.65391 0.58 81.606-2.0618 (bar) How should I fix this error? Any suggestions for improvement will really help me. Many thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 = sd ; stochastic leap-frog integrator dt = 0.002 nsteps = 150 ; 3 ns comm-mode = Linear; remove center of mass translation nstcomm = 100 ; frequency for center of mass motion removal ; Output control nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy= 5000 nstxout-compressed = 5000 ; Bond parameters continuation= yes; formerly known as 'unconstrained-start' - useful for exact continuations and reruns constraint_algorithm= lincs ; holonomic constraints constraints = h-bonds ; bonds to H are constrained lincs_iter = 1 ; accuracy of LINCS ; Neighborsearching and short-range nonbonded interactions cutoff-scheme= verlet nstlist = 20 ns_type = grid rlist= 1.2 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Electrostatics coulombtype = PME rcoulomb = 1.2 pme-order = 4; interpolation order for PME (default is 4) fourierspacing = 0.16 ; grid spacing for FFT ewald-rtol = 1e-6 ; relative strength of the Ewald-shifted direct potential at rcoulomb ewald_geometry = 3d ; Ewald sum is performed in all three dimensions ; van der Waals vdwtype = cutoff vdw-modifier = Potential-shift-Verlet verlet-buffer-tolerance = 2.5e-04 rvdw = 1.2 DispCorr = EnerPres ; apply long range dispersion corrections for Energy and Pressure ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc-grps = system ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 298.15 ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman pcoupltype = isotropic; uniform scaling of box vectors tau_p = 2.0 ; time constant (ps) ref_p = 1.0 ; reference pressure (bar) compressibility = 4.5e-05 ; isothermal compressibility of water (bar^-1) ; velocities gen_vel = no ; Velocity generation is on (if gen_vel is 'yes', continuation should be 'no') gen_seed = -1 ; Use random seed gen_temp = 298.15 ; Free energy control stuff free_energy = yes init_lambda_state= 10 delta_lambda = 0 calc_lambda_neighbors= 1; only immediate neighboring windows ; Vectors of lambda specified here ; Each combination is an index that is retrieved from init_lambda_state for each simulation vdw_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 coul_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 restraint_lambdas= 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ; Options for the decoupling sc-alpha = 0.5 sc-coul = no ; linear interpolation of Coulomb (none in this case) sc-power = 1 sc-sigma = 0.3 nstdhdl = 100 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 Any help would really be appreciated. Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 ( dihedral3) has 4 elements Select a group: 2 Selected 2: 'dihedral3' I get a warning as below:- Warning: calculating fractions as defined in this program makes sense for Ryckaert Bellemans dihs. only. Ignoring -of What does it mean? Can anyone please help me to understand? I am using gromacs 2020 Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 --- Pressure -0.2923431.360.92448.84635 (bar) I selected 1 bar ref pressure. Why is it going negative how should I fix it? I need your kind suggestions. Thanks in advance. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 rmsf1000ps.xvg -ox average1000ps.pdb -res -n index.ndx I am confused between using gmx rmsf and gmx cluster for getting average structure for clustering should I do the following? gmx cluster -f md_1000ps.xtc -s md.tpr -n index.ndx -av average1000ps.pdb Can you please correct me. Thanks in advance. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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. https://www.dropbox.com/sh/1ff45is9412dld4/AACDXjV0T47P01RgCJ1Baccca?dl=0 My dihedral angles have a multiplicity of 1 as mentioned below:- [ dihedral_restraints ] ; aiajakal type phiA dphiAfcA phiBdphiB fcB 72743133 1 146.72 0.0 0 146.72 0.0 41.840 7574 3127 1 173.10 0.0 0 173.10 0.0 41.840 7574 3125 1 158.21 0.0 0 158.21 0.0 41.840 However, in gromacs manual, I read this:- *Counting transitions only works for dihedrals with multiplicity 3* Am I doing something wrong? How should I measure dihedral restraint over time? Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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. https://www.dropbox.com/home/dihedral_angles My dihedral angles have a multiplicity of 1 as mentioned below:- [ dihedral_restraints ] ; aiajakal type phiA dphiAfcA phiBdphiB fcB 72743133 1 146.72 0.0 0 146.72 0.0 41.840 7574 3127 1 173.10 0.0 0 173.10 0.0 41.840 7574 3125 1 158.21 0.0 0 158.21 0.0 41.840 However, in gromacs manual, I read this:- *Counting transitions only works for dihedrals with multiplicity 3* Am I doing something wrong? How should I measure dihedral restraint over time? Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 restraints [ bonds ] ;ij type r0A r1A r2AfcAr0B r1B r2BfcB 712910 0.403 0.403 10.0 0.00.403 0.403 10.0 4184.000 [ angle_restraints ] ; aiajakal typethA fcAmultA thB fcB multB 29716971 1 104.92 0.01 104.92 41.840 1 71293129 1 147.02 0.01 147.02 41.840 1 [ dihedral_restraints ] ; aiajakal typephiA dphiA fcAphiB dphiB fcB 69712931 1146.72 0.00.0 146.72 0.0 41.840 7271 2931 1 17.55 0.00.017.55 0.0 41.840 7271 2925 1 173.10 0.00.0 173.10 0.0 41.840 However, after energy minimization, I observed that my restraints are not working and I find the following change:- bonds changed from 0.403 *0.401* angles:- 104.92 changed to *107.98* 147.02 changed to *152.76* dihedrals:- 146.72 changed to *141.72* 17.55 changed to 2*2.13* 173.10 changed to *174.23* The fluctuation in restraints goes on increasing till the production run which shows that my restraints are not working. How should I work with these so that they may not change much? Do I need to increase force for restraints if yes then how much increase? any idea? I have tried these simulations with position restraints. Is the method of putting restraints correct or should I try some other? I have to apply these in the free energy calculation which already crashed because of restraint failure. I would really be thankful for your kind suggestions, please. Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 options, How can I identify these groups show which part of the system. I want to calculate the dihedral angle as a function of time in the simulation. Group 0 ( Phi=0.0_3_0.65) has 228 elements Group 1 ( Phi=0.0_1_0.84) has 8 elements Group 2 ( Phi=0.0_2_0.84) has 8 elements Group 3 ( Phi=0.0_3_1.67) has16 elements Group 4 ( Phi=0.0_3_0.67) has52 elements Group 5 ( Phi=0.0_1_1.05) has96 elements Group 6 ( Phi=0.0_3_0.70) has 4 elements Group 7 (Phi=180.0_2_10.46) has32 elements Group 8 ( Phi=0.0_1_8.37) has16 elements Group 9 ( Phi=0.0_2_8.37) has 8 elements Group10 ( Phi=0.0_2_1.13) has 8 elements Group11 ( Phi=0.0_3_1.76) has 8 elements Group12 (Phi=180.0_1_1.88) has 4 elements Group13 (Phi=180.0_2_6.61) has 4 elements Group14 (Phi=180.0_3_2.30) has 4 elements Group15 ( Phi=0.0_1_3.35) has 4 elements Group16 (Phi=180.0_3_0.33) has 4 elements Group17 (Phi=180.0_2_15.17) has96 elements Group18 ( Phi=0.0_3_0.75) has 8 elements Group19 (Phi=180.0_2_1.05) has20 elements Group20 (Phi=180.0_1_0.84) has20 elements Group21 ( Phi=0.0_3_0.63) has32 elements Group22 ( Phi=0.0_2_3.35) has12 elements Group23 ( Phi=0.0_3_0.67) has28 elements Group24 ( Phi=0.0_3_0.70) has20 elements Group25 ( Phi=0.0_3_0.60) has24 elements Group26 ( Phi=0.0_2_4.92) has24 elements Group27 ( Phi=0.0_3_0.65) has96 elements Group28 ( Phi=0.0_3_1.60) has24 elements Group29 ( Phi=0.0_3_1.60) has12 elements Group30 (Phi=180.0_2_0.42) has12 elements Group31 ( Phi=0.0_3_0.75) has12 elements I tried gmx chi also by the following command:- gmx chi -s md.gro -f md.xtc -all 1 -o dihedral.xvg The out put file indicate following information xaxis label "Residue" yaxis label "S2" What is S2 on y-axis. How should I interpret it? Could anyone please help me with this? I would really appreciate your kind suggestions. Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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. 0. 1ACE HC4 0.000 0.000 0.000 0. 0. 0. 1ACE C5 0.000 0.000 0.000 0. 0. 0. 1ACE O6 0.000 0.000 0.000 0. 0. 0. 2PHE N7 5.066 4.671 6.042 0.2692 -0.2632 0.1330 2PHE H8 5.027 4.600 5.982 -1.5227 1.0889 -0.3963 2PHE CA9 5.013 4.811 6.023 0.0535 0.3709 0.0960 2PHE HA 10 5.058 4.868 6.105 -1.0081 1.0531 0.2242 2PHE CB 11 5.052 4.871 5.883 -0.0860 0.7332 0.2870 2PHEHB1 12 4.990 4.822 5.809 1.1212 -0.4628 0.0312 2PHEHB2 13 5.153 4.841 5.853 0.2157 2.3973 -0.5141 2PHE CG 14 5.062 5.017 5.867 0.0161 0.4565 0.5724 2PHECD1 15 4.951 5.101 5.874 -0.1757 -0.2234 -0.3056 2PHEHD1 16 4.855 5.054 5.884 -0.9265 1.6156 2.3658 2PHECE1 17 4.958 5.242 5.856 -0.3304 0.7195 0.1599 2PHEHE1 18 4.866 5.298 5.857 0.2928 1.7852 -0.4831 2PHE CZ 19 5.085 5.297 5.832 -0.3945 -1.0394 -0.7463 2PHE HZ 20 5.101 5.404 5.842 -0.5983 -1.2279 3.1660 2PHECE2 21 5.200 5.216 5.830 -0.1669 -0.6131 1.1550 2PHEHE2 22 5.293 5.264 5.804 -1.0122 1.2508 1.4080 2PHECD2 23 5.186 5.075 5.852 0.3885 0.2183 -0.6920 2PHEHD2 24 5.276 5.015 5.847 -0.0823 -0.3875 -3.1559 2PHE C 25 4.859 4.799 6.042 0.1650 -0.6772 0.7098 2PHE O 26 4.794 4.721 5.968 0.0339 0.0386 -0.1578 3NME N 27 0.000 0.000 0.000 0. 0. 0. 3NME H 28 0.000 0.000 0.000 0. 0. 0. 3NME CT 29 0.000 0.000 0.000 0. 0. 0. 3NME H1 30 0.000 0.000 0.000 0. 0. 0. 3NME H1 31 0.000 0.000 0.000 0. 0. 0. 3NME H1 32 0.000 0.000 0.000 0. 0. 0. 4G6P P 33 5.063 5.809 5.979 0.5468 0.1315 -0.0198 4G6PO1P 34 5.208 5.823 5.982 0.3151 -0.5087 0.1960 4G6PO2P 35 5.020 5.704 6.075 0.0937 -0.0791 -0.0538 4G6PO3P 36 5.028 5.939 6.039 -0.2953 0.3030 -0.2016 4G6P C1 37 4.985 5.671 5.430 0.5407 0.1917 0.2635 4G6P O1 38 5.118 5.662 5.388 -0.4011 0.4548 -0.8044 4G6P C2 39 4.889 5.558 5.383 0.3352 0.1447 0.3610 4G6P O2 40 4.876 5.546 5.239 -0.2019 -0.6192 -1.0434 4G6P C3 41 4.753 5.566 5.458 0.0668 0.4155 -0.3386 4G6P O3 42 4.674 5.438 5.425 -0.8214 0.3092 -0.1367 4G6P C4 43 4.783 5.561 5.611 0.3702 -0.3821 -0.5929 4G6P O4 44 4.661 5.608 5.676 -0.1025 0.6063 -0.0795 4G6P C5 45 4.890 5.667 5.654 -0.3851 0.4555 -0.1137 4G6P O5 46 5.006 5.658 5.573 -0.0288 0.1296 -0.6207 4G6P C6 47 4.935 5.670 5.809 -0.1636 0.0426 0.3771 4G6P O6 48 5.001 5.791 5.841 0.2972 -0.6933 -0.1489 4G6P H1 49 4.939 5.768 5.412 2.0772 1.3511 2.0534 4G6P H2 50 4.932 5.464 5.418 0.0848 -0.0506 0.1425 4G6P H3 51 4.706 5.660 5.427 0.9723 0.2387 -2.4228 4G6P H4 52 4.804 5.459 5.646 -0.3467 -0.2084 0.3693 4G6P H5 53 4.845 5.766 5.640 -0.6619 0.2119 -1.0742 4G6PH61 54 5.002 5.587 5.833 2.3826 1.5930 -0.8342 4G6PH62 55 4.851 5.665 5.878 1.0230 1.5442 2.0329 4G6PHO1 56 5.160 5.619 5.465 0. 23 -0.1270 -1.6233 4G6PHO2 57 4.816 5.469 5.232 -0.0502 -0.7762 -0.6581 4G6PHO3 58 4.671 5.441 5.328 0.3044 0.1862 -0.1954 4G6PHO4 59 4.649 5.553 5.755 -1.5501 2.1018 0.8000 Could you please suggest how should I do that? Thanks 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 r2BfcB 712910 0.403 0.403 10.0 0.00.403 0.403 10.0 4184.000 [ angle_restraints ] ; aiajakal typethA fcAmultA thB fcB multB 29716971 1 104.92 0.01 104.92 41.840 1 71293129 1 147.02 0.01 147.02 41.840 1 [ dihedral_restraints ] ; aiajakal typephiA dphiA fcAphiB dphiB fcB 69712931 1146.72 0.00.0 146.72 0.0 41.840 7271 2931 1 17.55 0.00.017.55 0.0 41.840 7271 2925 1 173.10 0.00.0 173.10 0.0 41.840 However, after energy minimization, I observed that my restraints are not working and I find the following change:- bonds changed from 0.403 *0.413* angles:- 104.92 changed to *109.24* 147.02 changed to *147.65* dihedrals:- 146.72 changed to *133.39* 17.55 changed to *12.94* 173.10 changed to *-166.16* How should I work with these so that they may not change much? Dihedrals seem to be changing more than bonds and angles. I have to apply these in the free energy calculation which already crashed because of restraint failure. I would really be thankful for your kind suggestions, please. Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 CA PHE A 1 1.462 0.000 0.000 1.00 0.00 C ATOM 3 C PHE A 1 1.902 0.000 1.473 1.00 0.00 C ATOM 4 O PHE A 1 1.105 0.000 2.411 1.00 0.00 O ATOM 5 CB PHE A 1 2.020 1.225 -0.743 1.00 0.00 C ATOM 6 CG PHE A 1 3.442 1.037 -1.219 1.00 0.00 C ATOM 7 CD2 PHE A 1 4.512 1.642 -0.547 1.00 0.00 C ATOM 8 CE2 PHE A 1 5.823 1.440 -0.982 1.00 0.00 C ATOM 9 CZ PHE A 1 6.074 0.642 -2.097 1.00 0.00 C ATOM 10 CE1 PHE A 1 5.015 0.044 -2.777 1.00 0.00 C ATOM 11 CD1 PHE A 1 3.705 0.238 -2.340 1.00 0.00 C ATOM 12 H PHE A 1 -0.467 0.280 0.859 1.00 0.00 H ATOM 13 HA PHE A 1 1.790 -0.939 -0.463 1.00 0.00 H ATOM 14 HB1 PHE A 1 1.956 2.118 -0.106 1.00 0.00 H ATOM 15 HB2 PHE A 1 1.405 1.454 -1.623 1.00 0.00 H ATOM 16 HD2 PHE A 1 4.334 2.273 0.322 1.00 0.00 H ATOM 17 HE2 PHE A 1 6.649 1.912 -0.456 1.00 0.00 H ATOM 18 HZ PHE A 1 7.094 0.492 -2.441 1.00 0.00 H ATOM 19 HE1 PHE A 1 5.208 -0.570 -3.654 1.00 0.00 H ATOM 20 HD1 PHE A 1 2.885 -0.231 -2.885 1.00 0.00 H ATOM 21 HN PHE A 1 -0.339 0.853 -0.435 1.00 0.00 H ATOM 22 2HN PHE A 1 -0.339 -0.853 -0.435 1.00 0.00 H ATOM 23 OXT PHE A 1 3.231 -0.000 1.717 1.00 0.00 O1- However, it claims that in the chosen force field there is no residue type for 'PHE' as a standalone (starting & ending) residue I am using AMBER99SB-ILDN force field for protein. I have looked into the force field both CPHE and NPHE are different as below:- [ CPHE ] [ atoms ] NN -0.38210 1 HH0.26810 2 CACT -0.18250 3 HAH1 0.10980 4 CBCT -0.09590 5 HB1HC 0.04430 6 HB2HC 0.04430 7 CGCA 0.05520 8 CD1CA -0.13000 9 HD1HA 0.1408010 CE1CA -0.1847011 HE1HA 0.1461012 CZCA -0.0944013 HZHA 0.1280014 CE2CA -0.1847015 HE2HA 0.1461016 CD2CA -0.1300017 HD2HA 0.1408018 CC0.7660019 OC1O2 -0.8026020 OC2O2 -0.8026021 [ bonds ] N H NCA CAHA CACB CA C CB HB1 CB HB2 CBCG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1CZ CZHZ CZ CE2 CE2 HE2 CE2 CD2 CD2 HD2 C OC1 C OC2 -C N [ impropers ] -CCA N H CA OC1 C OC2 CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CE1 CE2CZHZ CD1CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2CGCB [ NPHE ] [ atoms ] NN3 0.17370 1 H1H0.19210 2 H2H0.19210 3 H3H0.19210 4 CACT 0.07330 5 HAHP 0.10410 6 CBCT 0.03300 7 HB1HC 0.01040 8 HB2HC 0.01040 9 CGCA 0.0031010 CD1CA -0.1392011 HD1HA 0.1374012 CE1CA -0.1602013 HE1HA 0.1433014 CZCA -0.1208015 HZHA 0.1329016 CE2CA -0.1603017 HE2HA 0.1433018 CD2CA -0.1391019 HD2HA 0.1374020 CC0.6123021 OO -0.5713022 [ bonds ] NH1 NH2 NH3 NCA CAHA CACB CA C CB HB1 CB HB2 CBCG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1CZ CZHZ CZ CE2 CE2 HE2 CE2 CD2 CD2 HD2 C O C+N [ impropers ] CA+N C O CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CE1 CE2CZHZ CD1CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2CGCB How should I build it. Thanks. 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
[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 command : gmx editconf -f rescloselig.gro -o rescloseligbox.gro -bt cubic -d 1.2 Can you please suggest me how should I fix it. Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 file:- 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. 0. 1ACE HC4 0.000 0.000 0.000 0. 0. 0. 1ACE C5 0.000 0.000 0.000 0. 0. 0. 1ACE O6 0.000 0.000 0.000 0. 0. 0. 2PHE N7 5.066 4.671 6.042 0.2692 -0.2632 0.1330 2PHE H8 5.027 4.600 5.982 -1.5227 1.0889 -0.3963 2PHE CA9 5.013 4.811 6.023 0.0535 0.3709 0.0960 2PHE HA 10 5.058 4.868 6.105 -1.0081 1.0531 0.2242 2PHE CB 11 5.052 4.871 5.883 -0.0860 0.7332 0.2870 2PHEHB1 12 4.990 4.822 5.809 1.1212 -0.4628 0.0312 2PHEHB2 13 5.153 4.841 5.853 0.2157 2.3973 -0.5141 2PHE CG 14 5.062 5.017 5.867 0.0161 0.4565 0.5724 2PHECD1 15 4.951 5.101 5.874 -0.1757 -0.2234 -0.3056 2PHEHD1 16 4.855 5.054 5.884 -0.9265 1.6156 2.3658 2PHECE1 17 4.958 5.242 5.856 -0.3304 0.7195 0.1599 2PHEHE1 18 4.866 5.298 5.857 0.2928 1.7852 -0.4831 2PHE CZ 19 5.085 5.297 5.832 -0.3945 -1.0394 -0.7463 2PHE HZ 20 5.101 5.404 5.842 -0.5983 -1.2279 3.1660 2PHECE2 21 5.200 5.216 5.830 -0.1669 -0.6131 1.1550 2PHEHE2 22 5.293 5.264 5.804 -1.0122 1.2508 1.4080 2PHECD2 23 5.186 5.075 5.852 0.3885 0.2183 -0.6920 2PHEHD2 24 5.276 5.015 5.847 -0.0823 -0.3875 -3.1559 2PHE C 25 4.859 4.799 6.042 0.1650 -0.6772 0.7098 2PHE O 26 4.794 4.721 5.968 0.0339 0.0386 -0.1578 3NME N 27 0.000 0.000 0.000 0. 0. 0. 3NME H 28 0.000 0.000 0.000 0. 0. 0. 3NME CT 29 0.000 0.000 0.000 0. 0. 0. 3NME H1 30 0.000 0.000 0.000 0. 0. 0. 3NME H1 31 0.000 0.000 0.000 0. 0. 0. 3NME H1 32 0.000 0.000 0.000 0. 0. 0. 4G6P P 33 5.063 5.809 5.979 0.5468 0.1315 -0.0198 4G6PO1P 34 5.208 5.823 5.982 0.3151 -0.5087 0.1960 4G6PO2P 35 5.020 5.704 6.075 0.0937 -0.0791 -0.0538 4G6PO3P 36 5.028 5.939 6.039 -0.2953 0.3030 -0.2016 4G6P C1 37 4.985 5.671 5.430 0.5407 0.1917 0.2635 4G6P O1 38 5.118 5.662 5.388 -0.4011 0.4548 -0.8044 4G6P C2 39 4.889 5.558 5.383 0.3352 0.1447 0.3610 4G6P O2 40 4.876 5.546 5.239 -0.2019 -0.6192 -1.0434 4G6P C3 41 4.753 5.566 5.458 0.0668 0.4155 -0.3386 4G6P O3 42 4.674 5.438 5.425 -0.8214 0.3092 -0.1367 4G6P C4 43 4.783 5.561 5.611 0.3702 -0.3821 -0.5929 4G6P O4 44 4.661 5.608 5.676 -0.1025 0.6063 -0.0795 4G6P C5 45 4.890 5.667 5.654 -0.3851 0.4555 -0.1137 4G6P O5 46 5.006 5.658 5.573 -0.0288 0.1296 -0.6207 4G6P C6 47 4.935 5.670 5.809 -0.1636 0.0426 0.3771 4G6P O6 48 5.001 5.791 5.841 0.2972 -0.6933 -0.1489 4G6P H1 49 4.939 5.768 5.412 2.0772 1.3511 2.0534 4G6P H2 50 4.932 5.464 5.418 0.0848 -0.0506 0.1425 4G6P H3 51 4.706 5.660 5.427 0.9723 0.2387 -2.4228 4G6P H4 52 4.804 5.459 5.646 -0.3467 -0.2084 0.3693 4G6P H5 53 4.845 5.766 5.640 -0.6619 0.2119 -1.0742 4G6PH61 54 5.002 5.587 5.833 2.3826 1.5930 -0.8342 4G6PH62 55 4.851 5.665 5.878 1.0230 1.5442 2.0329 4G6PHO1 56 5.160 5.619 5.465 0. 23 -0.1270 -1.6233 4G6PHO2 57 4.816 5.469 5.232 -0.0502 -0.7762 -0.6581 4G6PHO3 58 4.671 5.441 5.328 0.3044 0.1862 -0.1954 4G6PHO4 59 4.649 5.553 5.755 -1.5501 2.1018 0.8000 However, it still claims the same error. How should I add this in force field file? How can I use -ter command that it can add N and C termini itself to the residue? I would really thankful for your suggestions. Thanks. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to set restraints in free energy calculation?
Dear Gromacs users I am doing a free energy calculation of the protein-ligand complex. During decoupling of the ligand vdw forces from protein, I have selected 21 different lambda windows between 0-1. I have put distance angle and dihedral restraints to keep the ligand in its position but in some of my lamda windows, the residue restrained with ligand crashes and generates different PDB structures. The residue of protein on which I put restraints for ligand brreaks apart and simulation crashes in lambda windows 0,1,2,4,8,9,11,12,13,17,18 however in windows 3,5,6,10, 14,15,19,20 it works well. My restraint section in topology is as below:- ; distance restraints [ bonds ] ;i j type r0A r1A r2AfcAr0B r1B r2B fcB 3437 790810 0.474 0.474 10.0 0.00.474 0.474 10.0 4184.000 [ angle_restraints ] ; aiajakal typethA fcAmultA thB fcB multB 3437 7908 7905 7908 1110.00 0.01 110.0041.840 1 7908 3437 3439 3437 1152.50.01 152.5 41.840 1 [ dihedral_restraints ] ; aiajakal typephiAdphiA fcAphiB dphiB fcB 7905 7908 3437 3439 1140.19 0.00.0140.190.0 41.840 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 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.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to fix restraints in free energy calculation?
Dear Gromacs users I am doing a free energy calculation of the protein-ligand complex. During decoupling of the ligand vdw forces from protein, I have selected 21 different lambda windows between 0-1. I have put distance angle and dihedral restraints to keep the ligand in its position but in some of my lamda windows, the residue restrained with ligand crashes and generates different PDB structures. It crashes in lambda windows 0,1,2,4,8,9,11,12,13,17,18 however in windows 3,5,6,10, 14,15,19,20 it works well. My restraint section in topology is as below:- ; distance restraints [ bonds ] ;i j type r0A r1A r2AfcAr0B r1B r2B fcB 3437 790810 0.474 0.474 10.0 0.00.474 0.474 10.0 4184.000 [ angle_restraints ] ; aiajakal typethA fcAmultA thB fcB multB 3437 7908 7905 7908 1110.00 0.01 110.0041.840 1 7908 3437 3439 3437 1152.50.01 152.5 41.840 1 [ dihedral_restraints ] ; aiajakal typephiAdphiA fcAphiB dphiB fcB 7905 7908 3437 3439 1140.19 0.00.0140.190.0 41.840 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 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.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] putting step wise constraints in energy minimization
Thank you, Justin, I am still confused about constraints other than position restraints. As mentioned https://www.quora.com/q/gnvbdldrivyzzipw/Use-of-constraints-in-molecular-dynamics Should I use constraints also for my system to converge better? As I am doing energy minimization in two steps using steep emtol =100 and constraints= all-bonds, which converges in 9116 steps Step Time 9115 9115.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.35583e+034.93367e+031.88532e+042.36071e+026.91634e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.12823e+043.37615e+05 -6.30626e+03 -2.68202e+065.72973e+03 Potential Pres. DC (bar) Pressure (bar) -2.24140e+060.0e+00 -2.56682e+04 Steepest Descents converged to Fmax < 100 in 9116 steps Potential Energy = -2.2414020e+06 Maximum force = 9.0994179e+01 on atom 76219 Norm of force = 3.3411843e+00 But the second minimization which I am doing in using steep integrator and emtol= 10 and constraints=none shows that:- Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 10 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy or turn off constraints altogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 315 steps, but did not reach the requested Fmax < 10. Potential Energy = -2.2420480e+06 Maximum force = 2.9302316e+02 on atom 4379 Norm of force = 3.5330992e+00 Finished mdrun on rank 0 Sun Feb 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_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 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.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to apply constraints in energy minimization
Dear Gromacs users I am trying to run a protein-ligand free energy calculation in which I initially run MD for 3 ns without free energy calculation and took these coordinates for free energy in which I am doing two-step energy minimization. Firstly at steepest decent with force tolerance of 100 with 2 nsteps which converges to in 7992 steps as mentioned below:- Energies (kJ/mol) Bond Restraint Pot. AngleProper Dih. Improper Dih. 1.21424e+039.53698e+014.72990e+031.83362e+041.86005e+02 LJ-14 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) 6.81666e+037.15551e+043.32691e+05 -6.56537e+03 -2.69738e+06 Coul. recip.Angle Rest. Dih. Rest. Potential Pres. DC (bar) 4.52484e+036.92787e+002.04511e+02 -2.26358e+060.0e+00 Pressure (bar)dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl -2.68131e+040.0e+000.0e+006.26922e+03 -1.62832e+03 dVrestraint/dl Constr. rmsd 0.0e+002.65292e-06 *Steepest Descents converged to Fmax < 100 in 7992 stepsPotential Energy = -2.2635825e+06Maximum force = 9.0506676e+01 on atom 16669Norm of force = 3.6179803e+00* Step Time 2470 2470.0 Energies (kJ/mol) Bond Restraint Pot. AngleProper Dih. Improper Dih. 7.44151e+049.26252e+014.47510e+041.83016e+041.95586e+02 LJ-14 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) 6.77053e+037.14269e+044.17453e+05 -6.56537e+03 -3.03191e+06 Coul. recip.Angle Rest. Dih. Rest. Potential Pres. DC (bar) 4.48733e+036.63779e+002.08432e+02 -2.40037e+060.0e+00 Pressure (bar)dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl -7.77641e+010.0e+000.0e+006.49503e+03 -1.88623e+03 dVrestraint/dl 0.0e+00 For the second minimization, I am using l-bfgs integrator at force tolerance 10 with 5 nsteps. I get the following message:- *Energy minimization has stopped, but the forces have not converged to therequested precision Fmax < 10 (which may not be possible for your system). * Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. Low-Memory BFGS Minimizer converged to machine precision in 2471 steps, but did not reach the requested Fmax < 10. Potential Energy = -2.4003668e+06 Maximum force = 2.1663138e+02 on atom 1093 Norm of force = 3.8024703e+00 Performed 2565 energy evaluations in total. But my system crashes at nvt step generating 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! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to fix error: Some of these results violate the Second Law of Thermodynamics
Dear Gromacs users I am doing free energy calculation of a ligand with protein. When I do gmx bar it gives me the following error:- Temperature: 298.15 K Detailed results in kT (see help for explanation): lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/- 0 13.29 0.061.28 0.101.37 0.081.54 0.09 1 21.41 0.040.47 0.050.31 0.050.77 0.03 2 30.88 0.060.09 0.020.06 0.010.41 0.06 3 40.67 0.03 -0.01 0.03 -0.01 0.030.25 0.01 4 50.50 0.010.11 0.000.10 0.000.22 0.01 5 60.33 0.01 -0.04 0.01 -0.07 0.030.21 0.03 6 70.27 0.020.07 0.040.04 0.020.22 0.03 7 80.11 0.030.05 0.020.04 0.010.16 0.01 8 90.11 0.01 -0.09 0.02 -0.10 0.020.17 0.01 9 100.08 0.020.12 0.010.12 0.010.20 0.00 10 11 -0.04 0.03 -0.01 0.03 -0.01 0.030.18 0.01 11 12 -0.09 0.030.06 0.030.05 0.030.19 0.02 12 13 -0.02 0.03 -0.12 0.03 -0.12 0.030.23 0.01 13 14 -0.01 0.030.17 0.030.16 0.030.28 0.02 14 15 -0.06 0.03 -0.09 0.03 -0.09 0.030.25 0.01 15 16 -0.04 0.030.13 0.040.13 0.040.29 0.01 16 17 -0.15 0.030.04 0.010.04 0.010.24 0.01 17 18 -0.14 0.030.01 0.020.01 0.020.25 0.01 18 19 -0.07 0.03 -0.01 0.01 -0.08 0.020.27 0.01 19 20 -0.05 0.010.18 0.000.09 0.000.28 0.00 WARNING: Some of these results violate the Second Law of Thermodynamics: This is can be the result of severe undersampling, or (more likely) there is something wrong with the simulations. Final results in kJ/mol: point 0 - 1, DG 8.14 +/- 0.14 point 1 - 2, DG 3.50 +/- 0.09 point 2 - 3, DG 2.19 +/- 0.14 point 3 - 4, DG 1.66 +/- 0.07 point 4 - 5, DG 1.24 +/- 0.02 point 5 - 6, DG 0.83 +/- 0.02 point 6 - 7, DG 0.66 +/- 0.06 point 7 - 8, DG 0.28 +/- 0.08 point 8 - 9, DG 0.28 +/- 0.03 point 9 - 10, DG 0.19 +/- 0.05 point 10 - 11, DG -0.10 +/- 0.08 point 11 - 12, DG -0.22 +/- 0.07 point 12 - 13, DG -0.05 +/- 0.08 point 13 - 14, DG -0.03 +/- 0.08 point 14 - 15, DG -0.16 +/- 0.07 point 15 - 16, DG -0.10 +/- 0.07 point 16 - 17, DG -0.37 +/- 0.07 point 17 - 18, DG -0.35 +/- 0.08 point 18 - 19, DG -0.17 +/- 0.06 point 19 - 20, DG -0.13 +/- 0.02 total 0 - 20, DG 17.29 +/- 0.47 I have read in the link that I should not have negative entropy values in my simulation https://www.mail-archive.com/gmx-users@gromacs.org/msg55772.html. Can 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! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 *, gmx_mdoutf *, int, int, const char *, gmx_mtop_t *, t_inputrec *, long, em_state_t *, t_state *, ObservablesHistory *) *Assertion failed:Condition: bX* The code below assumes that (with domain decomposition), x is collected to state_global in the call above. I could get a post regarding its fixing https://redmine.gromacs.org/issues/2554 Could you please suggest me why is this happening? and how should I fix it. Thanks & 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 anyone please suggest me how to solve this error? I have tried to use -nt 2 -pin on in order to avoid domain decomposition. Looking forward to hearing from you. Thanks and 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fwd:
Energy minimization getting jumps 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. AngleProper Dih. Improper Dih. 1.20860e+031.65864e+004.67218e+031.83350e+041.87873e+02 LJ-14 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) 6.81295e+037.12692e+043.37954e+05 -6.56537e+03 -2.70668e+06 Coul. recip.Angle Rest. Dih. Rest. Potential Pres. DC (bar) 4.78029e+035.32468e+003.32764e+00 -2.26802e+060.0e+00 Pressure (bar)dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl -2.69428e+040.0e+000.0e+002.78529e+03 -1.65404e+02 dVrestraint/dl Constr. rmsd 0.0e+002.71623e-06 Step Time 1050110501.0 Step Time 1050210502.0 Step Time 1050310503.0 Step Time 1050410504.0 Step Time 1050510505.0 Step Time 1050610506.0 Step Time 1050710507.0 Step Time 1050810508.0 Step Time 1050910509.0 Step Time 1051010510.0 Step Time 1051110511.0 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 10 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 10512 steps, 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 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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. AngleProper Dih. Improper Dih. 1.20860e+031.65864e+004.67218e+031.83350e+041.87873e+02 LJ-14 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) 6.81295e+037.12692e+043.37954e+05 -6.56537e+03 -2.70668e+06 Coul. recip.Angle Rest. Dih. Rest. Potential Pres. DC (bar) 4.78029e+035.32468e+003.32764e+00 -2.26802e+060.0e+00 Pressure (bar)dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl -2.69428e+040.0e+000.0e+002.78529e+03 -1.65404e+02 dVrestraint/dl Constr. rmsd 0.0e+002.71623e-06 Step Time 1050110501.0 Step Time 1050210502.0 Step Time 1050310503.0 Step Time 1050410504.0 Step Time 1050510505.0 Step Time 1050610506.0 Step Time 1050710507.0 Step Time 1050810508.0 Step Time 1050910509.0 Step Time 1051010510.0 Step Time 1051110511.0 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 10 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 10512 steps, 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 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problem of lincs in free energy calculations
Dear Gromacs users During free energy calculation, I am getting lincs warning at MD run in some of Lambda windows. To cope with this I have reduced my time step to 1 fs rather than 2. Some of them converged but for others, it still gives lincs warning and generates different PDB structures. If the 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/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 equal number of atoms and charges as per my understanding. Could anyone please suggest me where I am committing any mistake? I will be really thankful. Thanks in advance. Sadaf 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! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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. The thing which is confusing me is how should I switch off any of the above parameters should all lambda should be set to 1 or zero? e.g for while transforming electrostaticss I am setting vdw_lambdas, coul_lambdas and restraint_lambdas as below:- vdw_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 coul_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 restraint_lambdas= 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 Is it the right way of doing this? I need your suggestions, please. Thanks 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 interactions, except for exclusions: Restraint Pot. atoms 3437 7908 global 3437 7908 --- Program: gmx mdrun, version 2018.1 Source file: src/gromacs/domdec/domdec_topology.cpp (line 436) MPI rank:0 (out of 2) Fatal error: 1 of the 64584 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (4.47682 nm) or the two-body cut-off distance (4.47682 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck Could anybody please suggest how should I fix this error? I would be really thankful. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 interactions, except for exclusions: Restraint Pot. atoms 3437 7908 global 3437 7908 --- Program: gmx mdrun, version 2018.1 Source file: src/gromacs/domdec/domdec_topology.cpp (line 436) MPI rank:0 (out of 2) Fatal error: 1 of the 64584 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (4.47682 nm) or the two-body cut-off distance (4.47682 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck Could anybody please suggest how should I fix this error? I would be really thankful. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 protein and ligand in order to add distance restraints between ligand and protein atoms however for decoupling ligand from protein I need a separate molecule type for the ligand. How should I set the system to avoid this problem? Thanks in advance. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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, when I look at the trajectory for these restraints, these values fluctuate during the course of trajectory. For example I kept distance between two atoms 4.08 but it ranges from 3.80 to 4.60 in trajectory. Similarly, dihedral angles vary more than 10 degrees. Is it right? should I go for free energy calculation? If not how should I fix this? I need your suggestions, please. Thanks 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 the following error:- Splitting chemical chains based on TER records or chain id changing. WARNING: Chain identifier 'A' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. There are 2 chains and 0 blocks of water and 490 residues with 7921 atoms chain #res #atoms 1 'A' 489 7894 2 'A' 1 27 All occupancies are one Opening force field file ./amber99sb-ildn.ff/atomtypes.atp Atomtype 86 Invalid format: -- Program: gmx pdb2gmx, version 2019.4 Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 745) Fatal error: Atom O in residue G6P 516 was not found in rtp entry G6P with 27 atoms while sorting atoms. Could you please suggest me what wrong I am doing in rtp file Thank you in advance 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 index number in combined topology; will it not affect these terms? Could you please explain a bit more? I have attached a ligand file for reference. Thanks in advance. 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 "amber99sb-ildn.ff/forcefield.itp" #include "atomtypes.itp" #include "Protein.itp" #include "lig1.itp" distance restraints [ bonds ] ;i j type r0A r1A r2AfcAr0B r1B r2B fcB 3437 343910 0.408 0.408 10.0 0.00.408 0.408 10.0 4184.000 [ angle_restraints ] ; aiajakal typethA fcAmultA thB fcB multB 3439 3437 3437 7908 1162.37 0.01 162.37162.37 1 3437 7908 7908 7906 1112.53 0.01 112.53112.53 1 [ dihedral_restraints ] ; aiajakal typephiA dphiA fcAphiB dphiB fcB 3439 3437 7908 7906 1118.72 0.00.0118.720.0 41.840 3437 7908 7906 7907 1-69.05 0.00.0-69.050.0 41.840 3430 3439 3437 7908 1178.56 0.00.0178.560.0 41.840 #include "lig2.itp" #include "lig3.itp" ; Include Position restraint file #ifdef POSRES #include "posre_complex.itp" #endif ; Include water topology #include "amber99sb-ildn.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" but it gives me the following error:- ERROR 1 [file complex.top, line 9]: Atom index (7908) in bonds out of bounds (1-7893). This probably means that you have inserted topology section "bonds" in a part belonging to a different molecule than you intended to. In that case, move the "bonds" section to the right molecule. How should I fix my topology file that I may not give this error? Many thanks in advance 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
