Re: [gmx-users] dssp error
Hi, I used to have similar problem. Try using double precision. Worked for me. Best Quoting Albert mailmd2...@gmail.com: hello: I am trying to run do_dssp by command: do_dssp -s md.tpr -f md.trr -b 400 -e 500 -o fws_ss.xpm but it said: Select a group: 1 Selected 1: 'Protein' There are 35 residues in your selected group trn version: GMX_trn_file (single precision) Reading frame 400 time 400.000 Back Off! I just backed up ddbXn2WY to ./#ddbXn2WY.1# --- Program do_dssp, VERSION 4.5.5 Source code file: do_dssp.c, line: 572 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddbXn2WY ddeWknkk /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It's just the way this stuff is done (Built to Spill) Rohit Arora Laboratoire de Biologie et de Pharmacologie Génétique Appliquée (CNRS UMR 8113) Ecole Normale Supérieure, Cachan France Bureau: +33 (0) 1 47 40 77 49 Portable: +33 (0) 6 23 85 12 46 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with simulation of Protein-DNA complex
Hi Tsjerk, I have checked and re-checked the structure and it seems fine. I also made sure to minimise the starting structure really well after pdb2gmx. Although it did not achive required precision, but machine precision instead. Also, the problem starts with the NVT, before that everythings seems to work fine. Could there be any other source of error? I am not able to figure it out. Many Thanks. Quoting Tsjerk Wassenaar tsje...@gmail.com: Hi Rohit, Have you checked the atoms around 3460? It seems there's something wrong with your starting structure. Cheers, Tsjerk On Feb 9, 2012 2:09 PM, rar...@ens-cachan.fr wrote: Hi Lina, I am sorry, I think I forgot to mention that I did perform energy minimisation using Steep-Descent for 5000 steps, before NVT. I was so engrossed in other details that I forgot to mention it! Quoting lina lina.lastn...@gmail.com: On Thu, Feb 9, 2012 at 8:44 PM, rarora@ens-cachan.f... Bureau: +33 (0) 1 47 40 77 49 Portable: +33 (0) 6 23 85 12 46 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-... Rohit Arora Laboratoire de Biologie et de Pharmacologie Génétique Appliquée (CNRS UMR 8113) Ecole Normale Supérieure, Cachan France Bureau: +33 (0) 1 47 40 77 49 Portable: +33 (0) 6 23 85 12 46 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problem with simulation of Protein-DNA complex
Dear Gromacs users, I have been trying to simulate a Protein-DNA complex using gromacs, but each time I have been facing problems. I would like to point out that both the Protein and DNA have been modeled and after that docked in order to obtain a complex. Following are the parameters I am using: Force-Field: amber99sb-ildn water model: TIP3P 40 NA ions were added in order to neutralise the complex-solvent system. Gromacs doesn't show any error up until I proceed to do nvt equilibriation. Following is nvt.mdp: title = PFV_DNA_NVT define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 100 ; 2 * 5 = 100 ps dt = 0.001 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracyi ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed It generates a tpr, but upon mpirun gives the following error: starting mdrun 'Protein in water' 100 steps, 1000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.027514, max 0.979682 (between atoms 3460 and 3461) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3455 3457 65.20.1542 0.2535 0.1526 3455 3456 33.30.1093 0.1322 0.1090 3457 3459 72.70.1105 0.1739 0.1090 3457 3458 65.70.1105 0.1588 0.1090 3460 3469 78.60.1409 0.2693 0.1400 3460 3461 78.80.1409 0.2772 0.1400 3461 3463 75.10.1406 0.1489 0.1400 3463 3465 37.20.1403 0.1756 0.1400 3463 3464 40.70.1083 0.1408 0.1080 3465 3467 35.50.1403 0.1733 0.1400 3467 3469 74.00.1405 0.1373 0.1400 3467 3468 42.90.1083 0.1433 0.1080 Wrote pdb files with previous and current coordinates Step 1, time 0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 364940.065742, max 11977066.00 (between atoms 3465 and 3466) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3475 3495 110.80.1526 20544.7148 0.1522 3475 3477 111.60.1529 20544.4336 0.1526 3475 3476 108.10.1094 20543.1309 0.1090 3477 3480 62.80.1527 4.6441 0.1526 3477 3479 57.50.1091 4.5683 0.1090 3477 3478 93.60.1091 4.6160 0.1090 3495 3497 138.10.1336 4.9133 0.1335 3495 3496 69.60.1230 4.9085 0.1229 3497 3499 40.20.1449 0.2036 0.1449 3497 3498 43.80.1010 0.1527 0.1010 3480 3483 35.60.1526 0.1902 0.1526 3480 3482 42.20.1090 0.1501 0.1090 3480 3481 41.70.1090 0.1485 0.1090 3453 3455 88.70.1701 117322.3672 0.1449 3453 3454 88.30.1035 65066.2227 0.1010 3455 3471 48.90.1763 171383.6562 0.1522 3455 3457 134.60.2535 572521.2500 0.1526 3455 3456 66.70.1322 143042. 0.1090 3457 3460 67.5
Re: [gmx-users] Problem with simulation of Protein-DNA complex
Hi Lina, I am sorry, I think I forgot to mention that I did perform energy minimisation using Steep-Descent for 5000 steps, before NVT. I was so engrossed in other details that I forgot to mention it! Quoting lina lina.lastn...@gmail.com: On Thu, Feb 9, 2012 at 8:44 PM, rar...@ens-cachan.fr wrote: Dear Gromacs users, I have been trying to simulate a Protein-DNA complex using gromacs, but each time I have been facing problems. I would like to point out that both the Protein and DNA have been modeled and after that docked in order to obtain a complex. Following are the parameters I am using: Force-Field: amber99sb-ildn water model: TIP3P 40 NA ions were added in order to neutralise the complex-solvent system. Gromacs doesn't show any error up until I proceed to do nvt equilibriation. Before the NVT, you may do some energy minimization. Following is nvt.mdp: title = PFV_DNA_NVT define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 100 ; 2 * 5 = 100 ps dt = 0.001 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracyi ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed It generates a tpr, but upon mpirun gives the following error: starting mdrun 'Protein in water' 100 steps, 1000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.027514, max 0.979682 (between atoms 3460 and 3461) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3455 3457 65.2 0.1542 0.2535 0.1526 3455 3456 33.3 0.1093 0.1322 0.1090 3457 3459 72.7 0.1105 0.1739 0.1090 3457 3458 65.7 0.1105 0.1588 0.1090 3460 3469 78.6 0.1409 0.2693 0.1400 3460 3461 78.8 0.1409 0.2772 0.1400 3461 3463 75.1 0.1406 0.1489 0.1400 3463 3465 37.2 0.1403 0.1756 0.1400 3463 3464 40.7 0.1083 0.1408 0.1080 3465 3467 35.5 0.1403 0.1733 0.1400 3467 3469 74.0 0.1405 0.1373 0.1400 3467 3468 42.9 0.1083 0.1433 0.1080 Wrote pdb files with previous and current coordinates Step 1, time 0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 364940.065742, max 11977066.00 (between atoms 3465 and 3466) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3475 3495 110.8 0.1526 20544.7148 0.1522 3475 3477 111.6 0.1529 20544.4336 0.1526 3475 3476 108.1 0.1094 20543.1309 0.1090 3477 3480 62.8 0.1527 4.6441 0.1526 3477 3479 57.5 0.1091 4.5683 0.1090 3477 3478 93.6 0.1091 4.6160 0.1090 3495 3497 138.1 0.1336 4.9133 0.1335 3495 3496 69.6 0.1230 4.9085 0.1229 3497 3499 40.2 0.1449 0.2036 0.1449 3497 3498 43.8 0.1010 0.1527 0.1010 3480 3483 35.6 0.1526 0.1902 0.1526 3480 3482 42.2 0.1090 0.1501 0.1090 3480 3481 41.7 0.1090
