[gmx-users] Normal Mode
Hello everyone. I am doing a Normal Mode analysis on a small polymer. Just 17 atoms in vacuo. It is well minimized. Norm and Max Force < 1e-4. I am doing the analysis on the full precision configuration using the -t option. I am getting 6 eigen frequencies and 5 eigenvalues near zero which is of course good. However, I am getting 16 eigenfrequencies from 5000 to 21,000 cm-1 with enormous eigenvalues. This does not appear correct. Any insights as to why gromacs is producing these would be appreciated. Dan Sponseller PhD candidate George Mason University. -- 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] Normal Mode Analysis
Hello. I am trying to do a Normal Mode Analysis of a polymer in water. I am running my minimization right now with -DFLEXIBLE defined. How do I exclude the water from the analysis. I only want the analysis done on the polymer. Dan Sponseller PhD student, George Mason University -- 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] editconf -density
You do not state your original density. But lets say you need to reduce volume 3% to get your correct density. Use: ediftconf -f solv_large.gro -o solv_large_scaled.gro -scale 1 1 0.97 Just do a quick side calculation for what you need and substitute in for 0.97. Dan On Aug 9, 2015, at 4:18 AM, James Lord jjamesgreen...@gmail.com wrote: Hi all, I have a solvent filled in a box of dimensions 12 12 12 (solv_large.gro). I want to adjust the density of system to 824 kg/m3. But I want editconf to just change the volume only by changing the z direction ? is that possible? I did ediftconf -f solv_large.gro -o solv_large_scaled.gro -density 824 But it changes the x,y,z to adjust the density. Is it possible to ask editconf to do this only by changing for example z? Cheers James -- 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. -- 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] Help me with energy groups please.
For my main MD experiment, I run just the energy group System. This is fine. Then I take one configuration and run a minimization. For the minimization, I have two energy groups: peg2000 (my polymer), and Water so that I can inspect interaction energies. Here is the output from gmx energy: Energy Average Err.Est. RMSD Tot-Drift --- Morse 13.8929 1192.2316 -69.4839 (kJ/mol) G96Angle347.715 62127.946 -413.973 (kJ/mol) Proper Dih. 128.924 0.551.13049 -3.826 (kJ/mol) LJ-14 71.4762 24.16065 -13.8959 (kJ/mol) Coulomb-14 988.758 0.12 0.239868 0.836523 (kJ/mol) LJ (SR) 3263212.9 5.9749 -20.3545 (kJ/mol) Coulomb (SR) -1.85621e+06 0.360.80798 -2.48026 (kJ/mol) Coul. recip.2094.03 0.015 0.0317153 0.0976681 (kJ/mol) LJ recip. -30437.1 0.0032 0.00707587 -0.0217548 (kJ/mol) Potential-1.55669e+06 78191.241 -523.261 (kJ/mol) Pressure -2.80437e+345.7e+27 1.27529e+28 3.80388e+28 (bar) #Surf*SurfTen-1.35113e+331.8e+29 3.66158e+29 1.18298e+30 (bar nm) Coul-SR:peg2000-peg2000 -1.85621e+06 0.360.80798 -2.48026 (kJ/mol) LJ-SR:peg2000-peg20003263212.9 5.9749 -20.3545 (kJ/mol) Coul-14:peg2000-peg2000 988.758 0.12 0.239868 0.836523 (kJ/mol) LJ-14:peg2000-peg2000 71.4762 24.16065 -13.8959 (kJ/mol) Coul-SR:peg2000-Water 0 0 0 0 (kJ/mol) LJ-SR:peg2000-Water 0 0 0 0 (kJ/mol) Coul-14:peg2000-Water 0 0 0 0 (kJ/mol) LJ-14:peg2000-Water 0 0 0 0 (kJ/mol) Coul-SR:Water-Water 0 0 0 0 (kJ/mol) LJ-SR:Water-Water 0 0 0 0 (kJ/mol) Coul-14:Water-Water 0 0 0 0 (kJ/mol) LJ-14:Water-Water 0 0 0 0 (kJ/mol) ddd It appears I have no interaction energy between my polymer and the water and there is no interaction energy intra-Water. This makes no sense! I am using the standard spce water witch does have partial charges and my polymer has partial charges. There should be coulomb interaction and there should always be LJ interaction. Help me figure this out please. Attached is my mdp file. Dan Sponseller ** Run Control ** integrator = steep nsteps = 1 comm-mode= Linear nstcomm = 100 ** Energy Minimization emtol= 0.001 emstep = 0.01 ** Output Control ** nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 0 nstcalcenergy= 1 nstenergy= 1 energygrps = peg2000 Water ** Neighbor Searching ** cutoff-scheme= Verlet nstlist = 20 ns_type = grid pbc = xyz periodic-molecules = no verlet-buffer-tolerance = 0.001 ** Electrostatics ** coulombtype = PME coulomb-modifier = Potential-shift-Verlet rcoulomb = 1.5 ** VdW ** vdwtype = PME vdw-modifier = Potential-shift-Verlet rvdw = 1.5 ** Ewald ** fourierspacing = 0.15 pme-order= 6 ewald-rtol = 1e-5 ** Temperature Coupling ** tcoupl = no ;tcoupl = v-rescale nsttcouple = -1 tc-grps = System tau-t= 1.0 ref-t= 300 ** Pressure Coupling ** pcoupl = no ;pcoupl = Parrinello-Rahman ;pcoupl = Berendsen pcoupltype = isotropic nstpcouple = -1 tau-p= 2.0 compressibility = 4.5e-5 ref-p= 1 refcoord-scaling = all ** Velocity Generation ** gen-vel = no gen-temp = 300 gen-seed = 4242 ** Bonds ** constraints = none morse= yes -- 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] all in one pc for MD simulation calculations
Hello. You do not provide enough detail for any type of answer. For example. I have run a small molecule (100 atoms) on my laptop and finished in an hour. I am currently running 7 atoms on a computing cluster with 128 CPUs and it will take a week or two. Dan George Mason University On Apr 16, 2015, at 10:49 AM, Atila Petrosian atila.petros...@gmail.com wrote: Dear gromacs users I have a question about computer which is needed for MD simulation by gromacs. Is an all in one pc appropriate for MD simulation? Any help will highly appreciated. -- 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. -- 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] Build-Gromacs installation error
You might not have MPI installed on your computer (or MPICH). However, sounds like you are installing this on a personal computer. You should turn off MPI as GROMACS’ internal thread MPI is excellent. You only need to turn on MPI if you are installing this on a cluster where multiple CPUs are used on separated PCs. If you really need external MPI, the wrapper compiler is usually called ‘mpicc’. So set all the cmake variables to this. Dan On Feb 6, 2015, at 1:01 AM, rahul dhakne rahuldhakn...@gmail.com wrote: Hello Everyone, I am trying to install Gromacs on my computer. But after I run *cmake ..* command it display error -- Enabling native GPU acceleration -- Could NOT find MPI_C (missing: MPI_C_LIBRARIES MPI_C_INCLUDE_PATH) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIBRARIES MPI_CXX_INCLUDE_PATH) CMake Error at cmake/gmxManageMPI.cmake:150 (message): MPI support requested, but no MPI compiler found. Either set the C-compiler (CMAKE_C_COMPILER) to the MPI compiler (often called mpicc), or set the variables reported missing for MPI_C above. Call Stack (most recent call first): CMakeLists.txt:464 (include) -- Configuring incomplete, errors occurred! See also /home/rose/Software/Gromacs/gromacs-5.0.4/build-gromacs/CMakeFiles/CMakeOutput.log. See also /home/rose/Software/Gromacs/gromacs-5.0.4/build-gromacs/CMakeFiles/CMakeError.log. -- - Rose -- 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. -- 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] Jump in temperature each time a new simulation is started.
Thank you for getting back to me. I understand the limited precision of the .gro file but it cannot explain such a large jump in the temperature. Other than the fact that I am starting a new simulation, the parameters in the .mdp file are the same as the ones that equilibrated and produced the .gro file. Below is my .mdp file. Thank you again. Daniel Sponseller PhD Candidate George Mason University ; This mdp file is for an NPT ensemble. ** Run Control ** integrator = md dt = 0.5 nsteps = 70 comm-mode= Linear nstcomm = 50 ** Output Control ** nstxout = 1 nstvout = 0 nstfout = 0 nstlog = 1000 nstcalcenergy= 20 nstenergy= 20 energygrps = System ** Neighbor Searching ** cutoff-scheme= Verlet nstlist = 40 nstcalclr= -1 ns_type = grid pbc = xyz periodic-molecules = no rlist= 4.0 rlistlong= -1 verlet-buffer-drift = -1 ** Electrostatics ** coulombtype = PME coulomb-modifier = Potential-shift rcoulomb = 3.8 ** VdW ** vdwtype = Cut-off vdw-modifier = Potential-shift rvdw = 3.8 ** Ewald ** fourierspacing = 0.15 pme-order= 6 ewald-rtol = 1e-5 ** Temperature Coupling ** tcoupl = v-rescale nsttcouple = -1 tc-grps = System tau-t= 1.0 ref-t= 400 ** Pressure Coupling ** ;pcoupl = no pcoupl = berendsen pcoupltype = isotropic nstpcouple = -1 tau-p= 2.0 compressibility = 4.5e-5 ref-p= 1 refcoord-scaling = all ** Velocity Generation ** gen-vel = no gen-temp = 400 gen-seed = 4242 ** Bonds ** constraints = none morse= yes On Dec 31, 2014, at 3:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/31/14 3:05 PM, Dan Sponseller wrote: Hello. Every time I start a new simulation from a conformation that has been well equilibrated, there is a jump in the temperature. For example, starting from a .gro file with velocities that was a well equilibrated system at 400K has initial temperature about 440K. I am not generating new velocities for the new simulation. This happens all the time. It is always about a 10% increase in the temperature. Has anyone else experienced this? Does anyone know what might be happening? Please post your full .mdp file; there are options relevant to proper continuation. Also, velocities in .gro files are limited in precision. It is much more reliable to restart using a checkpoint file (grompp -t *.cpt). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- 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] NPT Simulation average pressure lower than Reference set pressure
I would recommend 200,000 time steps to try to get accurate pressure readings. Pressure, I believe, is computed from the virial and can fluctuate a lot. Also, adjust nstcalcenergy and nstenergy to a small number, I use 10 to get more accurate pressure readings. You should have noticed the error estimate on your pressure is 6.2. That could put your actual pressure at 1. Dan Sponseller PhD student George Mason University On Oct 30, 2014, at 1:49 AM, Agnivo Gosai agnivogromac...@gmail.com wrote: Dear Users I have a DNA-Protein system and I use AMBER99SB-Parmbsc0 ff in GROMACS 4.5.7 single precision. My earlier work flow 1) Topology preparation 2) Box , Solvation and Ions 3) Energy minimization - Steepest descent 4) NVT equilibration using a V-rescale thermostat and ref temp = 300 K average temp = 299.7 K after 100 ps NVT sim. 5) Next is NPT sim ( with same thermostat on ) *Pressure Coupling part of npt.mdp file :* ; Pressure coupling is on pcoupl = Berendsen ; Pressure coupling on in NPT, also weak coupling pcoupltype = isotropic ; uniform scaling of x-y-z box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure (in bar) compressibility = 4.5e-5; isothermal compressibility, bar^-1 refcoord_scaling= com *Content of npt.log file :* Last step --- Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 1.05446e+041.32866e+046.07202e+025.40636e+034.12184e+04 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 1.46731e+05 -1.93498e+03 -1.23170e+06 -1.17442e+051.30130e+03 PotentialKinetic En. Total EnergyTemperature Pres. DC (bar) -1.13198e+062.06576e+05 -9.25405e+052.99973e+02 -7.72790e+01 Pressure (bar) Constr. rmsd -5.57060e+000.0e+00 *g_energy output of npt.edr :* A)Statistics over 50001 steps [ 0. through 100. ps ], 1 data sets All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift -- - Pressure-5.57066.284.808538.1219 (bar) (B)All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift -- - Density 1012.13 0.551.871723.17412 (kg/m^3) *My run parameters are :* ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs My reference pressure is 1 bar , the average pressure is -5.5 bar . I believe that the system failed to achieve the reference set pressure. *So should I carry out the simulation for a longer time ?? Or should I use a different barostat on the next NPT run or do it in a fresh NPT run.* *Kindly suggest.* Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- 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. -- 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] Bond Energy question.
Hello. I have completed a simulation with two polyethylene glycol (PEG) molecules and then minimized the final conformation. As a demonstration that the two molecules wish to stick together, I separate the two molecules manually and run a single minimization step. I inspect the energy log file since it reports the energies at step zero. I show that the Potential energy is higher in the separated molecules which completes the demonstration. However, I also notice that the G96Bond energy is almost double. Since the atoms within each molecule have not moved relative to each other at step zero, should not the bond energy not have changed? The G96Bond energy should just be reporting the interaction between bonded atoms, correct? Thanks for any insight. Dan Sponseller PhD student George Mason University -- 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] Positive Potential Energy.
Hello everyone. I am still fairly new to gromcs but I have researched this well. I am getting a positive potential energy (my bond energy is always positive) no matter how long I run my simulation. I also get this when doing minimizations. Even just one molecule set at know minimum conformation. I am running in vacuo with no pbc. I have read on the mail list that in vacuo can produce this? This doesn’t make sense as the molecule should fly apart with always positive PE. I have tried gromos ff and opsla ff. Both do this. A colleague of mine also gets this with his simulations although he reports negative potential when solvated. Any help would be appreciated or any explanation on how to interpret gromacs output on this. I would question gromacs’ abilities if it cannot give a reasonable potential energy for a simple system. Daniel Sponseller PhD student George Mason University -- 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] Gromacs 5.0 installation
Hello. Just take the .tar.gz on a thumb drive to your new machine and install from that. Note that this machine will already need to have all the prerequisites. If not, you will need to install those first: cmake gcc Don’t forget fftw lapack and blas. You can use the ones built in gromacs with appropriate cmake flags but they are slow. Dan GMU On Aug 7, 2014, at 2:01 AM, Fatemeh Dabbagh daba...@sums.ac.ir wrote: Hi everyone, I'm trying to install Gromacs 5.0 on a computer which has no network connection. It would be appreciated if some one tell me how this can be done! Regards Fatemeh -- 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. -- 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] Difficulty preparing a polymer (PEG) for simulation.
I’m trying to prepare PEG for simulation in gromacs and running into considerable difficulties. My PEG chain is HOC-COC-COC…...COC-COC-COH with appropriate hydrogens on the carbons. I am using the new CHARM36.ff Following the procedure for polymers, I added a beginning, and end, and a central chain piece to ‘merged.rtp’ and modified the atom names in the .pdb file to match. I have also added the residues to the ‘residuetypes.dat’ as Non-Protein (I have also tried listing it as a Protein). pdb2gmx claims I have169 missing atoms but will create the .gro and .top files anyway with the -missing parameter passed. The .gro file has all the atoms but the .top seems to be missing much information on bonds and angles. Probably no point in continuing but after a quick editconfig, grompp gives me a fatal error: Group Protein referenced in the .mdp file was not found in the index file. I am new to gromacs and would really appreciate help getting started on its use like this. Following is some of my data files. Daniel Sponseller PhD student Computational Science and Informatics George Mason University Snip from ‘merged.rtp’ ;Dan Sponseller ;Copying from DME below for the repeating chain for PEG. [ LIG ] [ atoms ] C1 CC32A -0.010 0 H11 HCA2A0.090 1 H12 HCA2A0.090 2 OO2 OC30A -0.340 3 C3 CC32A -0.010 4 H31 HCA2A0.090 5 H32 HCA2A0.090 6 [ bonds ] C1 -C3 C1 H11 C1 H12 C1 OO2 OO2C3 C3 H31 C3 H32 C3 +C1 ;Dan Sponseller ;Next, define begining of chain for PEG. CH2-OH from [ ETOH ] [ LIGb ] [ atoms ] OO1 OG311 -0.650 0 H11 HGP10.420 1 C3 CG3210.050 2 H31 HGA20.090 3 H32 HGA20.090 4 [ bonds ] OO1 H11 OO1C3 C3 H31 C3 H32 C3 +C1 ;Dan Sponseller ;Next, define ending of chain for PEG. CH2-OH from [ ETOH ] [ LIGe ] [ atoms ] C1 CG3210.050 0 H11 HGA20.090 1 H12 HGA20.090 2 OO2 OG311 -0.650 3 H21 HGP10.420 4 [ bonds ] C1 -C3 C1 H11 C1 H12 C1 OO2 OO2 H21 my modified ‘PEG.pdb’ file: COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL HETATM1 C1 LIGe1 -14.784 -1.665 0.506 1.00 0.00 C HETATM2 C3 LIG 2 -13.927 -1.410 -0.735 1.00 0.00 C HETATM3 OO2 LIG 2 -13.056 -0.302 -0.493 1.00 0.00 O HETATM4 H11 LIGe1 -15.383 -2.563 0.355 1.00 0.00 H HETATM5 H12 LIGe1 -14.137 -1.802 1.372 1.00 0.00 H HETATM6 H31 LIG 2 -13.333 -2.297 -0.956 1.00 0.00 H HETATM7 H32 LIG 2 -14.573 -1.185 -1.584 1.00 0.00 H HETATM8 C1 LIG 2 -12.207 0.022 -1.596 1.00 0.00 C HETATM9 C3 LIG 3 -11.325 1.216 -1.227 1.00 0.00 C HETATM 10 OO2 LIG 3 -10.441 0.845 -0.167 1.00 0.00 O HETATM 11 H12 LIG 2 -11.578 -0.836 -1.835 1.00 0.00 H HETATM 12 H11 LIG 2 -12.818 0.276 -2.463 1.00 0.00 H HETATM 13 H31 LIG 3 -10.741 1.519 -2.096 1.00 0.00 H HETATM 14 H32 LIG 3 -11.953 2.046 -0.903 1.00 0.00 H HETATM 15 C1 LIG 3 -9.568 1.894 0.257 1.00 0.00 C HETATM 16 C3 LIG 4 -8.673 1.387 1.389 1.00 0.00 C HETATM 17 OO2 LIG 4 -7.815 0.358 0.894 1.00 0.00 O HETATM 18 H11 LIG 3 -8.949 2.211 -0.582 1.00 0.00 H HETATM 19 H12 LIG 3 -10.160 2.738 0.611 1.00 0.00 H HETATM 20 H31 LIG 4 -8.070 2.210 1.772 1.00 0.00 H HETATM 21 H32 LIG 4 -9.294 0.988 2.192 1.00 0.00 H HETATM 22 C1 LIG 4 -6.933 -0.187 1.877 1.00 0.00 C HETATM 23 C3 LIG 5 -6.066 -1.274 1.239 1.00 0.00 C HETATM 24 OO2 LIG 5 -5.215 -0.687 0.252 1.00 0.00 O HETATM 25 H11 LIG 4 -6.294 0.603 2.270 1.00 0.00 H HETATM 26 H12 LIG 4 -7.517 -0.619 2.690 1.00 0.00 H HETATM 27 H32 LIG 5 -5.457 -1.751 2.007 1.00 0.00 H HETATM 28 H31 LIG 5 -6.707 -2.020 0.768 1.00 0.00 H HETATM 29 C1 LIG 5 -4.360 -1.621 -0.408 1.00 0.00 C HETATM 30 C3 LIG 6 -3.499 -0.885 -1.437
