[gmx-users] (no subject)
Dear GMX Users, I am wish to perform a conformational transition simulation using coarse-grained models (SBM http://smog-server.org/). I wanted to apply flooding to explore the conformational transition and have open-close transition my trajectory. But what I find is that when I start from a open-state, the system moves to the closed-state and just stays there forever (20 ns) simulation. I use the following command. make_edi -f eigenvec.trr -eig eigenval.xvg -s 1pdb.pdb -o sam.edi -flood 7-16 -tau 0 -Eflnull 450.0 -hessian -alpha 2 -ori 1pdb.pdb -T 50 the eigenvec.trr was generated from anisotropic network models. How should I organize the different parameters to effect this transition. As of now I am executing my commands (and also my understanding) are based on the following paper: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20473/abstract Best, nahren -- 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] Conformational transition using essential dynamics
Dear GMX Users, I am wish to perform a conformational transition simulation using coarse-grained models (SBM http://smog-server.org/). I wanted to apply flooding to explore the conformational transition and have open-close transition my trajectory. But what I find is that when I start from a open-state, the system moves to the closed-state and just stays there forever (20 ns) simulation. I use the following command. make_edi -f eigenvec.trr -eig eigenval.xvg -s 1pdb.pdb -o sam.edi -flood 7-16 -tau 0 -Eflnull 450.0 -hessian -alpha 2 -ori 1pdb.pdb -T 50 the eigenvec.trr was generated from anisotropic network models. How should I organize the different parameters to effect this transition. As of now I am executing my commands (and also my understanding) are based on the following paper: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20473/abstract Best, nahren -- 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] how to get Eigenvectors
Dear GMX Users, I performed an ANM calculation at http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi It returned me eigenvectors in the following format (where the second and third column represent first and second eigenvector) 1 0.010551 -0.048553 1 -0.022038 -0.042918 1 0.107906 0.045009 2 0.007908 -0.061543 2 -0.002990 -0.054203 2 0.109087 0.062326 . . I tried to convert them into trr file, so that I can use them for analysis and this is where I am stuck. I converted them to PDB and I loose out on the precision of coordinates. ATOM 1 CA LYS A 1 0.011 -0.022 0.108 1.00 10.00 C ATOM 2 CA ILE A 2 0.008 -0.003 0.109 1.00 10.00 C ATOM 3 CA GLU A 3 0.008 0.011 0.077 1.00 10.00 C I added the reference structure (the structure I submitted to the server as frame 1, time 0) to the above PDB file and used g_nmtraj to get the projection. Is there a better way to get the eigenvec.trr. The server also returns Hessian, so can I use this information to get the eigenvec.trr using g_nmeig, but I am not sure how the format of nm.mtx should be. Can someone advice me on how to proceed further. Sincerely, nahren -- 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] COM restraint similar to distance restraints
Sorry to bother you all once again. As there were no replies, I assume it is not possible to implement COM distance restraints in a way similar to distance restrains. nahren From: nahren manuel meetnah...@yahoo.com To: gromacs gromacs gmx-users@gromacs.org Sent: Monday, April 1, 2013 9:56 PM Subject: [gmx-users] COM restraint similar to distance restraints Dear Gromacs Users, I was wondering if there is a way to implement the COM distance restraints (which I presently apply using pull, and setting pull-rate =0.0) in way similar to distance restraints defining the lower up1 up2 (i.e harmonic restraint with a flat well). Any suggestion will be appreciated. Sincerely, nahren -- gmx-users mailing list gmx-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 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] COM restraint similar to distance restraints
Dear Gromacs Users, I was wondering if there is a way to implement the COM distance restraints (which I presently apply using pull, and setting pull-rate =0.0) in way similar to distance restraints defining the lower up1 up2 (i.e harmonic restraint with a flat well). Any suggestion will be appreciated. Sincerely, nahren -- 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] PMF when pulling in -Z direction
Dear Gromacs Users, I am trying to study ligand unbinding adopting Umbrella sampling (using Gmx 4.5.3). during my initial pull to generate configurations for umbrella windows I have pulled in the -Z direction, @ s0 legend 0 Z @ s1 legend 1 dZ 0. 7.37361 -0.33625 0.0200 7.37377 -0.33631 0.0400 7.37404 -0.33637 0.0600 7.3744 -0.33643 0.0800 7.37473 -0.33649 . . . . 321.0800 7.37523 -1.29949 321.1000 7.37442 -1.29955 321.1200 7.37374 -1.29961 321.1400 7.37355 -1.29967 321.1600 7.37404 -1.29973 321.1800 7.37491 -1.29979 321.2000 7.3757 -1.29985 321.2200 7.37608 -1.29991 321.2400 7.37595 -1.29997 321.2600 7.37518 -1.30003 321.2800 7.37395 -1.30009 . . .(so on) Now when I ran simulations in each umbrella windows, the PMF energies are in negative. My guess is that this is due to my initial setup, or is there something seriously wrong. And if i am right I should get the correct PMF by taking the negative of this PMF (or is it)?? - ; Pull code (pulling simulation) pull = constraint pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = Protein pull_group1 = MAL pull_rate1 = 0.005 ; pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 500 ; every 1 ps pull_nstfout = 500 ; every 1 ps - ; Pull code (Umbrella simulation) pull = umbrella pull_geometry = distance ; pull_dim = Y Y Y pull_start = yes ; pull_ngroups = 1 pull_group0 = Protein pull_group1 = MAL pull_rate1 = 0.000 ; pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 500 ; every 1 ps pull_nstfout = 500 ; every 1 ps Best, nahren-- 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] PMF when pulling in -Z direction
Hi Justin, If you observe my pulling simulation, you will see that the distances are (increasing) in the negative. Here is the PMF (image): http://www.flickr.com/photos/nahrenmascarenhas/6312990056/ this is not one expects in ligand unbinding. (of course these are from my initial simulations, approx. 1 ns runs in 5 windows) Best, nahren From: Justin A. Lemkul jalem...@vt.edu To: nahren manuel meetnah...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, November 4, 2011 7:44 PM Subject: Re: [gmx-users] PMF when pulling in -Z direction nahren manuel wrote: Dear Gromacs Users, I am trying to study ligand unbinding adopting Umbrella sampling (using Gmx 4.5.3). during my initial pull to generate configurations for umbrella windows I have pulled in the -Z direction, @ s0 legend 0 Z @ s1 legend 1 dZ 0. 7.37361 -0.33625 0.0200 7.37377 -0.33631 0.0400 7.37404 -0.33637 0.0600 7.3744 -0.33643 0.0800 7.37473 -0.33649 . . . . 321.0800 7.37523 -1.29949 321.1000 7.37442 -1.29955 321.1200 7.37374 -1.29961 321.1400 7.37355 -1.29967 321.1600 7.37404 -1.29973 321.1800 7.37491 -1.29979 321.2000 7.3757 -1.29985 321.2200 7.37608 -1.29991 321.2400 7.37595 -1.29997 321.2600 7.37518 -1.30003 321.2800 7.37395 -1.30009 . . .(so on) Now when I ran simulations in each umbrella windows, the PMF energies are in negative. My guess is that this is due to my initial setup, or is there something seriously wrong. And if i am right I should get the correct PMF by taking the negative of this PMF (or is it)?? So your PMF is negative, why is that a problem? A negative binding energy indicates favorability of binding. -Justin - ; Pull code (pulling simulation) pull = constraint pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = Protein pull_group1 = MAL pull_rate1 = 0.005 ; pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 500 ; every 1 ps pull_nstfout = 500 ; every 1 ps - ; Pull code (Umbrella simulation) pull = umbrella pull_geometry = distance ; pull_dim = Y Y Y pull_start = yes ; pull_ngroups = 1 pull_group0 = Protein pull_group1 = MAL pull_rate1 = 0.000 ; pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 500 ; every 1 ps pull_nstfout = 500 ; every 1 ps Best, nahren -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Umbrella sampling COM distance
Dear Gromacs Users, I am trying to study the free energy of binding in a protein-ligand complex. I use the following pull input in my mdp file: ; Pull code pull = umbrella pull_geometry = distance pull_dim = N Y N pull_start = yes pull_ngroups = 1 pull_group0 = Protein pull_group1 = GLC pull_rate1 = 0.005 pull_k1 = 1000 if I am pulling in 'Y' direction, is it necessary to make sure that the distance between the COM (of the protein and ligand) = distance between the Y coordinates, i.eY(pro)-Y(lig), ? VMD commands set pro [atomselect top protein] set glc [atomselect top resname GLC] set A [measure center $pro weight mass] 40.33518600463867 35.01163101196289 38.7291374206543 set B [measure center $glc weight mass] 40.591331481933594 39.440189361572266 38.494876861572266 vecdist $A $B 4.4421411021009884 Y(pro)-Y(lig) = 4.42855835 Best, nahren -- 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] center of box protein
Dear GMX users, I am trying to center my protein at the center of box using editconf. When I view the same using ngmx, the protein seems to lie outside the box neweditconf -f alapdb.pdb -bt cubic -o boxpdb.pdb -c -center -0.156 -0.061 0.084 -d 1.5 this one works, but the molecule is shifted. neweditconf -f alapdb.pdb -bt cubic -d 1.5 -o try.pdb I want my molecule (geometrical ) center to be the center of the box with -d 1.5. Best, nahren -- 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] Force components on ATOM XX
Dear Gromacs Users, Is it possible to get the forces (components, x,y, z) acting on each atom from the simulation or from the rerun. I need them to calculate the Hessian Similar to http://www.sciencedirect.com/science/article/pii/S0006349507715989 Best, nahren -- 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] entropy from eigenfrequency
Dear Gromacs Users,
I was just wondering if the formula and the units which I use for getting the
entropy is absolutely correct.
The eigenfrequency (v) in cm-1 are obtained from eigenfreq.xvg.( GMX ver 4.0.7,
using normal mode calculations)
TS = [alpha/exp(alpha)-1] - log[1-exp(-alpha)]
where alpha = (h*v)/kbT,
h=Planck's const. ; kb= Boltzmann Constant; T=temperature.
Does the unit conversion result TS is kJ/mol (I feel yes, but I want to be
sure)?
My values are,
T(D)S = 415305.23 (complex) - 315149.18 (protein1) - 100122.14 (protein2)
So, T(D)S = 33.91 kJ/mol
Best,
nahren
My above conclusions are based on Gromacs source code,
/* Gromacs units are kJ/(mol*nm*nm*amu),
* where amu is the atomic mass unit.
*
* For the eigenfrequencies we want to convert this to spectroscopic
absorption
* wavenumbers given in cm^(-1), which is the frequency divided by the speed
of
* light. Do this by first converting to omega^2 (units 1/s), take the square
* root, and finally divide by the speed of light (nm/ps in gromacs).
*/
factor_gmx_to_omega2 = 1.0E21/(AVOGADRO*AMU);
factor_omega_to_wavenumber = 1.0E-5/(2.0*M_PI*SPEED_OF_LIGHT);
for (i=0; i=(end-begin); i++)
{
value = eigenvalues[i];
if(value 0)
value = 0;
value=sqrt(value*factor_gmx_to_omega2)*factor_omega_to_wavenumber;
fprintf (out,%6d %15g\n,begin+i,value);
}
fclose(out);
--
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[gmx-users] Entropy by total atoms
Dear Gromacs Users, I am calculating entropy from QHA and Schlitters formula to determine the entropy change in my proteinA-proteinB complex. Since proA and proB are quite different in terms of number of residues, I am little confused if I should divide the entropy value with the number of atoms included for calculation (i have used only heavy atoms) Best, nahren -- 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] Translation motion during MD
Dear Gromacs Users, I am simulating a Membrane protein, the extracellular domain alone (since the structure of only extracellular domain is solved). So I will have to simulate the protein in such a way that only the translational motion is allowed but the rotational motions are prevented (which would mimic the behavior of the protein attached to the membrane). The protein is expected to former dimer and multimers on the cell surface, so I want to restrict motion only to 2D. This would give an idea as to how the protein clusters on the membrane surface (studying this multimerization looks too ambitious, but want to make an attempt). Best, nahren -- 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] Translation motion during MD
Dear Gromacs Users, Yes Justin I totally agree with you and your point is well taken. But given the fact that if i dont restrain the protein, they rotate and I dont get the formation of clusters. Yes, i do want to protein to rotate in the plane of the membrane, but not the rotation that membrane-proximal become membrane -distal (this flipping rotation, if I may call like that) Another alternate I was thinking was to do a steered MD, but since there is no clue which part (which domain in the protein) form cluster, this method doesn't help either. Is applying semiisotropic pressure a good idea ? similar to what one would do in membrane simulation. Best, nahren --- On Thu, 11/11/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Translation motion during MD To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, November 11, 2010, 4:14 PM nahren manuel wrote: Dear Gromacs Users, I am simulating a Membrane protein, the extracellular domain alone (since the structure of only extracellular domain is solved). So I will have to simulate the protein in such a way that only the translational motion is allowed but the rotational motions are prevented (which would mimic the behavior of the protein attached to the membrane). I don't understand how you conclude that your protein shouldn't rotate. Even if the transmembrane portion was there, the protein could certainly rotate in the plane of the membrane. The protein is expected to former dimer and multimers on the cell surface, so I want to restrict motion only to 2D. This would give an idea as to how the protein clusters on the membrane surface (studying this multimerization looks too ambitious, but want to make an attempt). I suppose you could place a weak position restraint on all atoms in the z-dimension only. I would seriously question the validity of doing so, though. If you force a system into a preconceived behavior that masks other missing information, I'd say you're just causing the events to happen, not allowing them to occur naturally. You're also causing unnatural forces between the membrane and the protein. If the membrane deforms or undulates, the protein cannot accommodate this change. This is true no matter how you restrict this 2-D motion, and I think it would be a serious problem. -Justin Best, nahren -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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 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] continue Prod run from NPT eq
Dear Gromacs Users, I am using ver 4.5.1. I completed a 500 ps run of NPT (the mdp file is below). after when i try to do a prod run with both velocity and pressure read from the output of NPT, I get a error newgrompp -f eq3npt.mdp -o eq3npttpr.tpr -p dimertop.top -c eq2nptpdb.pdb -t eq2npttrr.trr -e eq2nptedr.edr ** READ 3 BOX VELOCITIES FROM eq2nptedr.edr --- Program newgrompp, VERSION 4.5.1 Source code file: enxio.c, line: 1022 Fatal error: Could not find energy term named 'Xi-0-Protein' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I cannot judge where I go wrong. Kindly help. Best, nahren *** mdp file *** define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 25 ; 2 * 25 = 500 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 0.2 ps nstvout = 500 ; save velocities every 0.2 ps nstenergy = 250 ; save energies every 0.2 ps nstlog = 500 ; update log file every 0.2 ps ; Bond parameters continuation = yes ; 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 accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.5 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = cut-off ; Particle Mesh Ewald for long-range electrostatics ; ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein SOL ; three coupling groups - more accurate tau_t = 0.2 0.2 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 5.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions ;pbc = xyz ; 3-D PBC ; Dispersion correction ;DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = system -- 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] ARG Charmm gmx 4.5.1
Dear Gromacs Users, I am using plain cutoff for my 12-mer protein. The grompp reports ARG to have a big charge group. this was also highlighted in the following mail http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html I was just think if changing the charges on these atoms would help, from 13 CT2 1 ARG CD 4 0.2 12.011 ; qtot 1.2 14 HA 1 ARG HD1 4 0.09 1.008 ; qtot 1.29 15 HA 1 ARG HD2 4 0.09 1.008 ; qtot 1.38 16 NC2 1 ARG NE 4 -0.7 14.007 ; qtot 0.68 17 HC 1 ARG HE 4 0.44 1.008 ; qtot 1.12 18 C 1 ARG CZ 4 0.64 12.011 ; qtot 1.76 19 NC2 1 ARG NH1 4 -0.8 14.007 ; qtot 0.96 20 HC 1 ARG HH11 4 0.46 1.008 ; qtot 1.42 21 HC 1 ARG HH12 4 0.46 1.008 ; qtot 1.88 22 NC2 1 ARG NH2 4 -0.8 14.007 ; qtot 1.08 23 HC 1 ARG HH21 4 0.46 1.008 ; qtot 1.54 24 HC 1 ARG HH22 4 0.46 1.008 ; qtot 2 to CD 0.18 HD1 0.06 HD2 0.06 NE -0.7 HE 0.4 CZ 0.6 NH1 -0.8 HH11 0.5 HH12 0.5 NH2 -0.8 HH21 0.5 HH22 0.5 The above transformation of charges seems reasonable. Would like to know if this is okay... Best, nahren -- 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] pdb2gmx -chainsep vs -merge
Dear Gromacs Users, thanks for all your suggestions. Tsjerk, I did try your idea, but unfortunately doesn't seem to work. the pdb file is shared here : http://www.4shared.com/account/file/ijofD83b/DIMER.html newpdb2gmx -f DIMER.pdb -chainsep interactive -ignh Fatal error: Atom OXT in residue CYS 283 was not found in rtp entry CYS with 11 atoms while sorting atoms. . Part of the file is pasted below: ATOM 2836 N CYS R 283 -27.431 91.636 -6.099 1.00 0.00 N ATOM 2837 H CYS R 283 -27.855 90.779 -6.392 1.00 0.00 H ATOM 2838 CA CYS R 283 -26.033 91.780 -6.514 1.00 0.00 C ATOM 2839 CB CYS R 283 -25.500 90.433 -7.060 1.00 0.00 C ATOM 2840 SG CYS R 283 -25.121 89.114 -5.829 1.00 0.00 S ATOM 2841 HG CYS R 283 -24.270 89.566 -4.957 1.00 0.00 H ATOM 2842 C CYS R 283 -25.867 92.922 -7.562 1.00 0.00 C ATOM 2843 OXT CYS R 283 -26.993 93.593 -7.927 1.00 0.00 O ATOM 2845 N LYS B 284 -23.431 108.789 63.478 1.00 0.00 N ATOM 2846 H1 LYS B 284 -23.779 109.339 64.238 1.00 0.00 H ATOM 2847 H2 LYS B 284 -23.156 109.392 62.730 1.00 0.00 H Best, nahren --- On Tue, 9/7/10, Tsjerk Wassenaar tsje...@gmail.com wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, September 7, 2010, 11:14 AM Hi, One work-around for the -chainsep situation you've observed is to remove or rename the terminal oxygen atoms (OXT) that pdb2gmx is complaining about when it tries to merge the chains. It should be taking care of that itself, but handling it yourself might help. pdb2gmx can probably rebuild the carboxyl oxygen. Keeping (one of the) OXT atoms and renaming it to O (keeping the fixed-column format correct) might be needed. There should be only one OXT per chain. Removing those seems like a good idea: sed -i '/^ATOM.*OXT/d' file.pdb (Remove all lines starting with ATOM and containing OXT, in the file) Hope it helps, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands -- gmx-users mailing list gmx-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 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] pdb2gmx -chainsep vs -merge
Dear Gromacs Users, Tsjerk, the original file did not contain OXT, as you can see, it has O1 O2, so I removed the O2 from the PDB and renamed O1 to OXT. ATOM 2841 HG CYS R 283 -24.270 89.566 -4.957 1.00 0.00 H ATOM 2842 C CYS R 283 -25.867 92.922 -7.562 1.00 0.00 C ATOM 2843 O1 CYS R 283 -26.993 93.593 -7.927 1.00 0.00 O ATOM 2844 O2 CYS R 283 -24.611 93.156 -8.027 1.00 0.00 O ATOM 2845 N LYS B 284 -23.431 108.789 63.478 1.00 0.00 N ATOM 2846 H1 LYS B 284 -23.779 109.339 64.238 1.00 0.00 H sed -i '/^ATOM.*O2/d' DIMER.pdb Am i going wrong here? the original PDB file is here : http://www.4shared.com/account/file/bTulGDPs/DIMER_FINAL.html Best, nahren --- On Tue, 9/7/10, Tsjerk Wassenaar tsje...@gmail.com wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, September 7, 2010, 12:22 PM Hi Nahren, Can you paste your actual command line where you used sed? Cheers, Tsjerk On Tue, Sep 7, 2010 at 12:11 PM, nahren manuel meetnah...@yahoo.com wrote: Dear Gromacs Users, thanks for all your suggestions. Tsjerk, I did try your idea, but unfortunately doesn't seem to work. the pdb file is shared here : http://www.4shared.com/account/file/ijofD83b/DIMER.html newpdb2gmx -f DIMER.pdb -chainsep interactive -ignh Fatal error: Atom OXT in residue CYS 283 was not found in rtp entry CYS with 11 atoms while sorting atoms. . Part of the file is pasted below: ATOM 2836 N CYS R 283 -27.431 91.636 -6.099 1.00 0.00 N ATOM 2837 H CYS R 283 -27.855 90.779 -6.392 1.00 0.00 H ATOM 2838 CA CYS R 283 -26.033 91.780 -6.514 1.00 0.00 C ATOM 2839 CB CYS R 283 -25.500 90.433 -7.060 1.00 0.00 C ATOM 2840 SG CYS R 283 -25.121 89.114 -5.829 1.00 0.00 S ATOM 2841 HG CYS R 283 -24.270 89.566 -4.957 1.00 0.00 H ATOM 2842 C CYS R 283 -25.867 92.922 -7.562 1.00 0.00 C ATOM 2843 OXT CYS R 283 -26.993 93.593 -7.927 1.00 0.00 O ATOM 2845 N LYS B 284 -23.431 108.789 63.478 1.00 0.00 N ATOM 2846 H1 LYS B 284 -23.779 109.339 64.238 1.00 0.00 H ATOM 2847 H2 LYS B 284 -23.156 109.392 62.730 1.00 0.00 H Best, nahren --- On Tue, 9/7/10, Tsjerk Wassenaar tsje...@gmail.com wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, September 7, 2010, 11:14 AM Hi, One work-around for the -chainsep situation you've observed is to remove or rename the terminal oxygen atoms (OXT) that pdb2gmx is complaining about when it tries to merge the chains. It should be taking care of that itself, but handling it yourself might help. pdb2gmx can probably rebuild the carboxyl oxygen. Keeping (one of the) OXT atoms and renaming it to O (keeping the fixed-column format correct) might be needed. There should be only one OXT per chain. Removing those seems like a good idea: sed -i '/^ATOM.*OXT/d' file.pdb (Remove all lines starting with ATOM and containing OXT, in the file) Hope it helps, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands -- gmx-users mailing list gmx-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 mailing list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands -Inline Attachment Follows- -- gmx-users mailing list gmx-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
Re: [gmx-users] intermolecular distance restrains
Dear Gromacs Users, Justin, I took your advice and using 4.5.1. I have attached the PDB file for your consideration. http://www.4shared.com/file/RwF_wuja/chainABCRST.html Command : newpdb2gmx -f chainABCRST.pdb -p dimertop.top -o dimerpdb.pdb -chainsep interactive -ignh 8: CHARMM27 all-atom force field (with CMAP) - version 2.0beta (forcefield selected) 6: None (water model) Reading chainABCRST.pdb... Read 6636 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. Merge chain ending with residue LEU144 (chain id 'A', atom 1444 OXT) with chain starting with residue LYS284 (chain id 'B', atom 1445 N)? [n/y] y Merge chain ending with residue LEU427 (chain id 'B', atom 2888 OXT) with chain starting with residue LYS567 (chain id 'C', atom 2889 N)? [n/y] y Merge chain ending with residue LEU710 (chain id 'C', atom 4332 OXT) with chain starting with residue CYS145 (chain id 'R', atom 1 N)? [n/y] n Merge chain ending with residue CYS283 (chain id 'R', atom 1400 OXT) with chain starting with residue CYS428 (chain id 'S', atom 1401 N)? [n/y] y Merge chain ending with residue CYS566 (chain id 'S', atom 2800 OXT) with chain starting with residue CYS711 (chain id 'T', atom 2801 N)? [n/y] y Program newpdb2gmx, VERSION 4.5.1 Source code file: pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue LEU 427 was not found in rtp entry LEU with 19 atoms while sorting atoms. * But this selection works (for the same above command, 1 ) Merge chain ending with residue LEU144 (chain id 'A', atom 1444 OXT) with chain starting with residue LYS284 (chain id 'B', atom 1445 N)? [n/y] y Merge chain ending with residue LEU427 (chain id 'B', atom 2888 OXT) with chain starting with residue LYS567 (chain id 'C', atom 2889 N)? [n/y] n Merge chain ending with residue LEU710 (chain id 'C', atom 4332 OXT) with chain starting with residue CYS145 (chain id 'R', atom 1 N)? [n/y] y Merge chain ending with residue CYS283 (chain id 'R', atom 1400 OXT) with chain starting with residue CYS428 (chain id 'S', atom 1401 N)? [n/y] n Merge chain ending with residue CYS566 (chain id 'S', atom 2800 OXT) with chain starting with residue CYS711 (chain id 'T', atom 2801 N)? [n/y] y * After ABC , I include a 'TER', then start chain RST, and make 'chainsep ter' 2. newpdb2gmx -f chainABCRSTter.pdb -p dimertop.top -o dimerpdb.pdb -chainsep ter -ignh Program newpdb2gmx, VERSION 4.5.1 Source code file: pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue LEU 427 was not found in rtp entry LEU with 19 atoms while sorting atoms. The residue are not in sequential Order , but i dont think that is the problem here. Thank you. Best, nahren --- On Fri, 9/3/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] intermolecular distance restrains To: Gromacs Users' List gmx-users@gromacs.org Date: Friday, September 3, 2010, 3:18 AM nahren manuel wrote: Dear Gromacs Users, The problem actually is mine is a hexamer, ARBSCT (chains). I want RST to be merged into a single molecular topology. I am either able to merge RS or ST or RT but not the trimer as such. How is the .pdb set up? Does it have both chain ID's and TER delimiters? What was your pdb2gmx command line? -Justin I am able to do with -merge in the previous (ver 4.0.7 of ) pdb2gmx. Best, nahren --- On *Thu, 9/2/10, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] intermolecular distance restrains To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, September 2, 2010, 8:09 PM nahren manuel wrote: Dear Gromacs Users, I am presently using gromacs4.5 beta(since I want implicit solvent). I No need to use a beta version, the official 4.5 has been released. wish to apply intermolecular distance restraints. To my surprise there is no merge option in pdb2gmx (although pdb2gnx -h, says it has). So is there a new alternative to create intermolecular distance restrains. Use pdb2gmx -chainsep. -Justin Best, nahren -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org /mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ
[gmx-users] intermolecular distance restrains
Dear Gromacs Users, I am presently using gromacs4.5 beta(since I want implicit solvent). I wish to apply intermolecular distance restraints. To my surprise there is no merge option in pdb2gmx (although pdb2gnx -h, says it has). So is there a new alternative to create intermolecular distance restrains. Best, nahren -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] intermolecular distance restrains
Dear Gromacs Users, The problem actually is mine is a hexamer, ARBSCT (chains). I want RST to be merged into a single molecular topology. I am either able to merge RS or ST or RT but not the trimer as such. I am able to do with -merge in the previous (ver 4.0.7 of ) pdb2gmx. Best, nahren --- On Thu, 9/2/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] intermolecular distance restrains To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, September 2, 2010, 8:09 PM nahren manuel wrote: Dear Gromacs Users, I am presently using gromacs4.5 beta(since I want implicit solvent). I No need to use a beta version, the official 4.5 has been released. wish to apply intermolecular distance restraints. To my surprise there is no merge option in pdb2gmx (although pdb2gnx -h, says it has). So is there a new alternative to create intermolecular distance restrains. Use pdb2gmx -chainsep. -Justin Best, nahren -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Re: Minimization before NMA
Dear Gromacs Users, Thanks for your Reply. Yes i did move forward to calculate the eigenvalues, as listed below. 1 -1.0096 2 -0.860704 3 -0.621409 4 -0.0477899 5 -7.98079e-07 6 -2.20151e-08 7 2.76454e-06 8 0.000416762 9 0.000621199 10 0.00206166 11 0.0256563 12 0.0287882 13 0.0341334 14 0.0540256 15 0.103671 16 0.107328 17 0.117916 18 0.152177 19 0.177111 20 0.204475 21 0.211167 22 0.249744 23 0.259533 24 0.26757 25 0.293689 . . . . the first six eigenvalues should ideally be close to zero, but I such high negative value confuses me a little. So does this indicate my normal mode calculation is imperfect ? Anyway these first 6 eigenvalues are infact not considered for calculation. The remaining eigenvalues are all non-negative. So I do not know if things are fine. I am repeating the procedure with another starting structure from the MD run (the lowest energy snapshot). Best, nahren --- On Tue, 8/3/10, Vitaly Chaban vvcha...@gmail.com wrote: From: Vitaly Chaban vvcha...@gmail.com Subject: [gmx-users] Re: Minimization before NMA To: gmx-users@gromacs.org Date: Tuesday, August 3, 2010, 1:53 AM nahren: Hmm... Why do you think Fmax=1.754e+00 is not enough for NMA? Dr. Vitaly Chaban I am unable to minimize a complex protein (Trimer-Trimer complex) to even less than Fmax=1.754e+00. I tried few tricks like performing MD for few steps etc, but it does not yield any results. I am sure there must be a way out. Can you please advice. Thanks for your attention. nahren -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Minimization before NMA
Dear Gromacs Users, I am unable to minimize a complex protein (Trimer-Trimer complex) to even less than Fmax=1.754e+00. I tried few tricks like performing MD for few steps etc, but it does not yield any results. I am sure there must be a way out. Can you please advice. Thanks for your attention. nahren -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Entropy from NMA
Dear Ran, I ran the whole NMA again and I found where I go wrong. I hope it will help others as well. (sorry for a big email) In steps 1 2 (of minimization) I kept the C-alpha frozen. 1. doublegrompp -f em1.mdp -c r1dodecapdb.pdb -p r1top.top -o em1tpr.tpr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em1tpr Steepest Descents converged to Fmax 100 in 2569 steps Potential Energy = -6.21296128286120e+03 Maximum force = 9.87358378592302e+01 on atom 701 Norm of force = 1.04875323563923e+01 2. doublegrompp -f em2.mdp -c em1tpr.gro -p r1top.top -o em2tpr.tpr -t em1tpr.trr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em2tpr Polak-Ribiere Conjugate Gradients converged to Fmax 1 in 6596 steps Potential Energy = -7.56682084795001e+03 Maximum force = 9.92719787231560e-01 on atom 1320 Norm of force = 6.47772253797808e-02 3. doublegrompp -f em3.mdp -c em2tpr.gro -p r1top.top -o em3tpr.tpr -t em2tpr.trr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em3tpr Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 writing lowest energy coordinates. Steepest Descents converged to machine precision in 3018 steps, but did not reach the requested Fmax 10. Potential Energy = -8.49398064549505e+03 Maximum force = 6.86336687926682e+01 on atom 935 Norm of force = 7.15798864024085e+00 4. doublegrompp -f em4.mdp -c em3tpr.gro -p r1top.top -o em4tpr.tpr -t em3tpr.trr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em4tpr Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 0.01 writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to machine precision in 21674 steps, but did not reach the requested Fmax 0.01. Potential Energy = -9.66058047638671e+03 Maximum force = 1.49342602818840e+00 on atom 590 Norm of force = 1.86576579430541e-01 5.doublegrompp -f em5.mdp -c em4tpr.gro -p r1top.top -o em5tpr.tpr -t em4tpr.trr ~/gmxdpr/bin/doublemdrun -v -deffnm em5tpr Low-Memory BFGS Minimizer converged to machine precision in 10346 steps, but did not reach the requested Fmax 0.0001. Potential Energy = -9.66337416273684e+03 Maximum force = 6.48625019025464e-04 on atom 581 Norm of force = 6.35632681200205e-05 6.doublegrompp -f em6.mdp -c em5tpr.gro -p r1top.top -o em6tpr.tpr -t em5tpr.trr Low-Memory BFGS Minimizer converged to machine precision in 3316 steps, but did not reach the requested Fmax 1e-08. Potential Energy = -9.66337416275038e+03 Maximum force = 6.48788529801368e-05 on atom 8 Norm of force = 6.56362137550289e-06 7. doublegrompp -f em7.mdp -c em6tpr.gro -p r1top.top -o em7tpr.tpr -t em6tpr.trr Low-Memory BFGS Minimizer converged to machine precision in 7530 steps, but did not reach the requested Fmax 1e-08. Potential Energy = -9.66337416275071e+03 Maximum force = 4.07762128402886e-07 on atom 10 Norm of force = 5.79534451487287e-08 8. doublegrompp -f em8.mdp -c em7tpr.gro -p r1top.top -o em8tpr.tpr -t em7tpr.trr Low-Memory BFGS Minimizer converged to Fmax 1e-08 in 5840 steps Potential Energy = -9.66337416275070e+03 Maximum force = 8.41750710592449e-09 on atom 521 Norm of force = 1.2888919393e-09 NMA 9. doublegrompp -f nma.mdp -t em8tpr.trr -c em8tpr.gro -p r1top.top -o nmatpr.tpr ~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr (a sinlge processor) ~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr it created only one nmatpr.mtx Maximum force: 8.41751e-09 Finished step 1400 out of 1400 It creates the output nmatpr.mtx nmatpr.edr etc Now I delete all nma files rm nmatpr.* (4 processor) mpirun -np 4 ~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr Maximum force: 8.41768e-09 Maximum force: 8.41768e-09 Maximum force: 8.41768e-09 Maximum force: 8.41768e-09 Finished step 1399 out of 1400 Writing Hessian... Writing Hessian... Writing Hessian... Finished step 1400 out of 1400 Writing Hessian... Back Off! I just backed up nmatpr.mtx to ./#nmatpr.mtx.2# It gives me negative eigenvalues. One would expect it should not create nmatpr.mtx.1 nmatpr.mtc.2 etc...since these files have been removed. Because it created multiple nmatpr.mtx file and backup one over another I am not sure If the problem occurs with my system , but other MPIRUN (with mdrun) do not create such backup. Best, nahren --- On Wed, 7/28/10, Ran Friedman r.fried...@bioc.uzh.ch wrote: From: Ran Friedman r.fried...@bioc.uzh.ch Subject: Re: [gmx-users] Entropy from NMA To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, July 28, 2010, 3:10 PM p.s. How big is this negative value? Ran Friedman wrote: Hi, Can you post the exact commands you used for EM and NMA? Ran nahren manuel wrote: Dear Gromacs Users, I am trying to calculate Entropy from Normal Mode Analysis. I minimized
Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ
Dear Tsjerk, The trjconv is not working, it is likely that i am not issuing the proper commands. --- My ndx file - - - Select group for output Group 0 ( System) has 2619 elements Group 1 ( Protein) has 2619 elements Group 2 ( Protein-H) has 2619 elements Group 3 ( C-alpha) has 873 elements Group 4 ( Backbone) has 2619 elements Group 5 ( MainChain) has 2619 elements Group 6 (MainChain+Cb) has 2619 elements Group 7 ( MainChain+H) has 2619 elements Group 8 ( SideChain) has 0 elements Group 9 ( SideChain-H) has 0 elements Group 10 (r_1-152_r_457-595) has 873 elements Group 11 (r_153-304_r_596-734) has 873 elements Group 12 (r_305-456_r_735-873) has 873 elements Group 13 ( a_1-456) has 456 elements Group 14 (a_1-456_a_1369-1785) has 873 elements Group 15 (a_457-912_a_1786-2202) has 873 elements Group 16 (a_913-1368_a_2203-2619) has 873 elements Group 17 (a_1-456_a_1369-1785_a_457-912_a_1786-2202_a_913-1368_a_2203-2619) has 2619 elements Kindly advice nahren --- On Mon, 5/10/10, nahren manuel meetnah...@yahoo.com wrote: From: nahren manuel meetnah...@yahoo.com Subject: Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, May 10, 2010, 3:50 PM Dear Tsjerk, No the problem was not with GROMACS. I have one structure as a X-ray and the other i created by homology modeling based on this structure. So the difference arose because my starting structures themselves were different. I did try trjconv with an index file , but it did not work out fine. I will check them once again before getting back. Thank you nahren --- On Mon, 5/10/10, Tsjerk Wassenaar tsje...@gmail.com wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, May 10, 2010, 3:35 PM Hi Nahren, You can do that using trjconv and an index file with the atom indices as they are in the order as they have to be. But is that really your problem? To understand what happened, it would help if you gave the series of commands that led to these results. Cheers, Tsjerk On Mon, May 10, 2010 at 11:42 AM, nahren manuel meetnah...@yahoo.com wrote: Dear Gromacs Users, I simulated two homologous (proteins) , and noticed after the simulation that in one trajectory, the protein is stored as ABCXYZ and in another it is as AXBYCZ. (where A, Z are chain information, ABC is a trimer and XYZ is another trimer, so the system is a trimer-trimer complex) I should not have any issues for most of my trajectory analysis. But when I wanted to get a correlation plots of the CA-CA from the covariance matrix, the plots cannot be compared, as the information in the trajectory is different. So is there a way that I can convert my trajectory from ABCXYZ to AXBYCZ. Thank you, nahren -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Trj conversion: ABCXYZ to AXBYCZ
Dear Gromacs Users, I simulated two homologous (proteins) , and noticed after the simulation that in one trajectory, the protein is stored as ABCXYZ and in another it is as AXBYCZ. (where A, Z are chain information, ABC is a trimer and XYZ is another trimer, so the system is a trimer-trimer complex) I should not have any issues for most of my trajectory analysis. But when I wanted to get a correlation plots of the CA-CA from the covariance matrix, the plots cannot be compared, as the information in the trajectory is different. So is there a way that I can convert my trajectory from ABCXYZ to AXBYCZ. Thank you, nahren -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ
Dear Tsjerk, No the problem was not with GROMACS. I have one structure as a X-ray and the other i created by homology modeling based on this structure. So the difference arose because my starting structures themselves were different. I did try trjconv with an index file , but it did not work out fine. I will check them once again before getting back. Thank you nahren --- On Mon, 5/10/10, Tsjerk Wassenaar tsje...@gmail.com wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, May 10, 2010, 3:35 PM Hi Nahren, You can do that using trjconv and an index file with the atom indices as they are in the order as they have to be. But is that really your problem? To understand what happened, it would help if you gave the series of commands that led to these results. Cheers, Tsjerk On Mon, May 10, 2010 at 11:42 AM, nahren manuel meetnah...@yahoo.com wrote: Dear Gromacs Users, I simulated two homologous (proteins) , and noticed after the simulation that in one trajectory, the protein is stored as ABCXYZ and in another it is as AXBYCZ. (where A, Z are chain information, ABC is a trimer and XYZ is another trimer, so the system is a trimer-trimer complex) I should not have any issues for most of my trajectory analysis. But when I wanted to get a correlation plots of the CA-CA from the covariance matrix, the plots cannot be compared, as the information in the trajectory is different. So is there a way that I can convert my trajectory from ABCXYZ to AXBYCZ. Thank you, nahren -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] -center -fit dodecahedron : dimer
Dear Gromacs Users, I am performing a MD simulation of a dimer in a dodecahedron box. The simulation stopped after 8 ns (power cut) and i had to restart to complete it fully to 12 ns. I then concatenated the two trajectories using trjcat trjconv -f promd.trr -s proem.tpr -pbc nojump -o nojump.xtc trjconv -f nojump.xtc -s proem.tpr -pbc mol -ur compact -center -boxcenter tric -o center.xtc trjconv -f center.xtc -s proem.tpr -fit rot+trans -o fit.xtc 1. The above procedures does not center the molecule in the box. 2. The box seems to shift from one corner to the center. Especially for the duration 8-12 ns (my restart run) I feel I am missing something here. Kindly advice. regards, nahren ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] -center -fit dodecahedron : dimer
Dear Gormacs User, I have now created a new tpr in which the protein is centered. trjconv -f promd.xtc -s tprdodecasolv.tpr -center -boxcenter tric -pbc mol -ur compact -o center.xtc trjconv -s tprdodecasolv.tpr -fit rot+trans -f center.xtc -o fit.xtc I see the dimer getting split in some of the frames of fit.xtc.? 2. The box seems to shift from one corner to the center. Especially for the duration 8-12 ns (my restart run) What do you mean with this? I actually see my dodeca box jumping from one end of the viewer to another ( in VMD as well as in ngmx) thanks for your attention and reply. regards nahren --- On Wed, 4/22/09, Tsjerk Wassenaar tsje...@gmail.com wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] -center -fit dodecahedron : dimer To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, April 22, 2009, 2:50 PM Hi Nahren, trjconv -f promd.trr -s proem.tpr -pbc nojump -o nojump.xtc trjconv -f nojump.xtc -s proem.tpr -pbc mol -ur compact -center -boxcenter tric -o center.xtc trjconv -f center.xtc -s proem.tpr -fit rot+trans -o fit.xtc 1. The above procedures does not center the molecule in the box. You first center and then do a fit. The fitted trajectory will only be centered if the reference (proem.tpr) is (and then you can skip the second step anyway). 2. The box seems to shift from one corner to the center. Especially for the duration 8-12 ns (my restart run) What do you mean with this? Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] PBC dodecahedron (corrected)
Dear Gromacs Users, I am having some trouble in viewing my molecule in VMD as a protein in dodecahedron. I did the following 1. trjconv -f promd.trr -o nojump.xtc -s promd.tpr -pbc nojump 2. trjconv -f nojump..xtc -s promd.tpr -o mdcenter.xtc -ur compact -pbc mol -center -boxcenter tric I have run my simulation for 12 ns (of a protein dimer ).. I see the box remain dodecahedron till about 5 ns after that the sides of the dodecahedron becomes unequal. i tried -pbc atom/whole etc, but does not help. Any advice on the issue will be truly helpful. regards, nahren ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] how to parametrize Phos. Thr TPO
Dear Gromacs Users, I am trying to simulate a protein whose Thr residues is phosphorylated. I did the following based on the earlier query regarding the same here is how I did it for phosphorylated Threonine. 1) open the appropriate .rtp file e.g. ffG43a1.rtp 2) make a copy of the existing entry for the residue you want to phosphorylate it. here are the notes I made as I did it...comments welcome if anyone doesnt like how I did it! ; TPO which follows is phosphorylated Threonine and was derived thus: ; 1) take THR entry ; 2) add P, O1P, O2P, O3P atoms ; 3) remove HG1 atom ; 4) assign partial charges to give an overall molecule -2 charge ; with this charge localised on the Phosphate group. ; 5) add bonds for OG1 to P and the OxPs. took bond tpyes from [ DADE ] ; 6) likewise took angle types from [ DADE ] ; 7) removed final dihedral which contained H1 (had considered changing it for ; P but dont want to limit Phoshphate group too much) 3) you will need to add the new residue to the file aminoacids.dat if you want the residue to be recognised as part of the protein in subsequent analysis. Make sure you increment the count on the top line of aminoacids.dat. dont put any comments in aminoacids.dat becuase it has unpredictable effects on results. 4) update the hydrogen database entry too if you are expecting pdb2gmx or protonate to work properly. I *think* that was it...! Paul Barrett but i get the following error * * * * * Generated 380 of the 1326 non-bonded parameter combinations ERROR 0 [file top_A.itp, line 16530]: No default Proper Dih. types ERROR 0 [file top_A.itp, line 16531]: No default Proper Dih. types Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 NOTE: System has non-zero total charge: -1.96e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 5789 # G96ANGLES: 8462 # PDIHS: 3040 # IDIHS: 2893 # LJ14: 9248 --- Program grompp, VERSION 3.3.2 Source code file: grompp.c, line: 1182 Fatal error: There were 2 errors in input file(s) --- Ich Bin Ein Berliner (J.F. Kennedy) * * * * * * Kindly advice nahren ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re (in reply to Tsjerk): [gmx-users] Porcupine Plots
Dear Dr. Tsjerk, thanks for your reply. I got the clue from your reply and i did the same via VMD. But can you please be little more speicific about Pymol. I am not quite used to that software. regards, nahren --- On Mon, 2/2/09, Tsjerk Wassenaar tsje...@gmail.com wrote: From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Porcupine Plots To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, February 2, 2009, 2:06 PM Hi Nahren, Gromacs does not include a tool for generation of porcupine plots. But if you're offered a means to do it through a webservice, all you really need is to take the extreme projections (two frames: g_anaeig -extr) and submit them. In a sense, you'll get the same thing if you load the extreme projections into pymol and use 'align extrA,extrB,object=displacement'. Then hiding one of the structures basically gives you a porcupine plot. Hope it helps, Tsjerk On Mon, Feb 2, 2009 at 6:28 AM, Mark Abraham mark.abra...@anu.edu.au wrote: nahren manuel wrote: Dear Gromacs Users, I have done PCA of my MD , I want to visually represent the motions in terms of porcupine plots. I came across Dynamite (web server) for this purpose. But it only considers 500 frames of the xtc file. Is there any other way how i could generate porcupine plots based on tools of GROMACS ? I've never heard of such plots - perhaps you should look for pointers wherever you came across them in the first place? Users on this list might help with some nuts and bolts, but first you need to make sure we can have access to useful information - like URLs and algorithm descriptions. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Porcupine Plots
Dear Gromacs Users, I have done PCA of my MD , I want to visually represent the motions in terms of porcupine plots. I came across Dynamite (web server) for this purpose. But it only considers 500 frames of the xtc file. Is there any other way how i could generate porcupine plots based on tools of GROMACS ? regards, nahren ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] about dumping the last frame
Dear Awasthi, go through GROMACS Introductory tutorial... trjconv -f abc.pdb -s abc.tpr -o 3frame.pdb -dump 3 You can also open the pdb file in VMD and save only the last frame SIMPLE ! nahren --- On Mon, 2/2/09, Shirin Awasthi shirin.mtech...@gmail.com wrote: From: Shirin Awasthi shirin.mtech...@gmail.com Subject: [gmx-users] about dumping the last frame To: gmx-users@gromacs.org Date: Monday, February 2, 2009, 12:00 PM Hi. I have a protein model in pdb format after trjconv command. it has 3 frames, that is 3 consecutive models of the same protein. how do i dump only the last frame as my final model? -- Shirin Awasthi M.Tech (CSB) Center for Computational Biology and Bioinformatics, School of Information Technology, Jawaharlal Nehru University, New Delhi, 110067 INDIA. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] ASP-LIG Interaction Energy : MDRUN
Dear Gromacs Users, I have just completed one (5ns ) mdrun. Now If i want to calculate the interaction energy between two residues, my ligand and ASP104, how should I go about calculating the same. The one option I know is by creating .ndx . But I did not expect this residue to play an important role when i started my simulation. So i did not include this protein residue ASP104 as a seperate group. Kindly advice. regards, nahren ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
Dear Vivek, you just have to download swisspdb and open your pdb file. Thats all you got to do and It is more than enough. If you have more than 2/3 residues missing then, make sure the Ramachandran plots are fine. Also try a simple minimization before begining gromacs. nahren --- On Tue, 8/12/08, vivek sharma [EMAIL PROTECTED] wrote: From: vivek sharma [EMAIL PROTECTED] Subject: Re: [gmx-users] Error in pdb2gmx.Atom CE2 not found in residue PHE270 while adding hydrogens To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, August 12, 2008, 6:34 PM Hi David, Thanx a lot again. can you please tell me the criteria or the standards to do such correction or can you suggest some link or tutorial for the same? whether swiss pdb can help in such cases? With Thanx, Vivek 2008/8/12 David van der Spoel [EMAIL PROTECTED] vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error. ... ... ... N-terminus: NH3+ C-terminus: COO- WARNING: atom CE2 not found in residue 270 while adding atom --- Program pdb2gmx, VERSION 3.3.3 Source code file: genhydro.c, line: 304 Fatal error: Atom CE2 not found in residue PHE270 while adding hydrogens --- I tried the same with different force field and water models, but getting the same error again and again. any suggestion will be highly appreciated. You have an incorrect pdb file. An atom is missing. You have to fix it yourself. With thanx, Vivek ___ gmx-users mailing list [EMAIL PROTECTED] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list [EMAIL PROTECTED] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Seperate rlist - Coulomb vdw
Dear Gromacs Users, I just wonder if it possible to define rlist = 0.9 rvdw = 1.2 vdwtype = cut-off rlist = 1.2 ; second rlist for rcoulomb coulombtype = cut-off rcoulomb = 1.5 I think calulation wise it doen't make a big change , but just the idea striked me so wanted to know... nahren ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Partial charges QM to GROMACS
Dear Gromacs Users, 1. I calculated the partial charges of my ligand using QM. Since GROMACS ignores the non-polar hydrogen, is it a good approximation to include the charges as it is from QM method to my ligand heavy atoms ?. 2. should i adjust that partial charges , If so how to do the same? regards, nahren ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Partial charges QM to GROMACS
Dear Dr. Lemkul, Thanks for the reply. Yes I am referring to GROMOS forcefield. So how should i treat my partial charges. Kindly advice. nahren --- On Fri, 7/11/08, Justin A. Lemkul [EMAIL PROTECTED] wrote: From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] Partial charges QM to GROMACS To: [EMAIL PROTECTED], Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, July 11, 2008, 7:25 PM Quoting nahren manuel [EMAIL PROTECTED]: Dear Gromacs Users, 1. I calculated the partial charges of my ligand using QM. Since GROMACS ignores the non-polar hydrogen, is it a good approximation to include the charges as it is from QM method to my ligand heavy atoms ?. Gromacs does no such thing! What you're referring to is the *Gromos* force field, which is an entirely separate idea. There are all-atom force fields for use with Gromacs - OPLS, Amber, and even CHARMM, if you're adventurous :-) What you need to be concerned with is whether or not these QM charges and methodology are compatible with your force field of choice. 2. should i adjust that partial charges , If so how to do the same? See above. -Justin regards, nahren Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Partial Charge of 1.11 ???
Dear Gromacs Users, I calculated Partial Charges for my Ligand which is Positively Charged. When I Do a 3-21G* partial charge assignment based , I get partial charge value of 1.1147 on one of the Carbon atoms. I am little confused about it. can partial charges be greater than 1.??? Kindly advice regards, nahren ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Partial Vs Formal Charges
Dear Gromacs USERs, My ligand, which contains a piperazine ring needs to be positively charged (+1). When I assign Gasteiger charges, it comes out to be -0.336 on the Nitrogen. But When I do a SEMI-EMPIRICAL PM3 to place my partial charge , it puts +0.733 on this atom. So does it mean it has put partial charge as (F.Charge - P. Charge). When I use InsightII (cff91 FF), the partial charge on this ligand was -0.556 and also it had a formal charge of +1. So kindly suggest me the best way out. Also, does gromacs takes formal charges automatically or is there a way to define the same. thanks nahren ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
