Re: [gmx-users] H2 topology
Dear Mark, Your suggestions were very helpful . As per the literature I am following , It is required that the dummy atom has mass 0 and charge -0.950.Hence , I created the following itp file with this in mind. ## ; topology for hydrogen. [ moleculetype ] ;namenrexcl H2 2 [ atoms ] ; nrtype resnr residuatomcgnr charge mass; total charge 1 H 1 H2 H1 1 0.475 1.00800 ; 0.00 2 H 1 H2 H2 1 0.475 1.00800 ; 0.00 3 DUM 1 H2 DUM 1 -0.950 0.0 ; 0.00 [ virtual_sites2 ] ; Site from funct a 3 1 2 1 0.074 [ constraints ] 1 2 2 0.074 ## But during energy minimization I encountered many problems. The errors are: ### error ## Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up em_ion_out.mdp to ./#em_ion_out.mdp.9# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 3 bonded neighbours molecule type 'Protein_B' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'H2' processing coordinates... double-checking input for internal consistency... Cleaning up constraints and constant bonded interactions with virtual sites renumbering atomtypes... converting bonded parameters... ERROR 1 [file 2frv_ion.top, line 40]: atom DUM (Res H2-6) has mass 0 ERROR 2 [file 2frv_ion.top, line 40]: atom DUM (Res H2-7) has mass 0 --- Program grompp_d, VERSION 4.0 Source code file: grompp.c, line: 940 Fatal error: There were 2 errors in input file(s) -- ### error Is this due to a problem in the .itp file? Even though i referred to the previous queries made in the forum , I was not able to get an answer, Please guide me as to where I have gone wrong . Thank You, jyotsna On Wed, 03 Feb 2010 22:42:09 +1100 Mark Abraham mark.abra...@anu.edu.au wrote: *This message was transferred with a trial version of CommuniGate(r) Pro* - Original Message - From: 011013021-Jyotsna 011013...@bioinfo.sastra.edu Date: Wednesday, February 3, 2010 21:48 Subject: Re: [gmx-users] H2 topology To: Discussion list for GROMACS users gmx-users@gromacs.org Dear David, Thanks for your reply. From your reply, I get the impression that the bond length of my hydrogen molecule gets adjusted duing minimization of the whole system ( protien+water+ inserted hydrogen molecule). But the issue impending is the insertion of the hydrogen molecule itself into the protein+water box created in previous step. For insertion/addition of hydrogen molecules I used the command: genbox_d -cp 2frv.conf.gro -o 2frv.solv.gro -p 2frv.top ci h2.gro nmol 100 What about a two-stage process? Do genbox -ci h2.gro -nmol 100 when there's no water, and then solvate *afterwards*. Or, generate solvent, and get a list of 100 random numbers in the right range, manually delete those water molecules to create interstices, update your [molecules] section, then use genconf -ci and equilibrate carefully to fix the density. Or, generate solvent for a box somewhat smaller than the one you want, use editconf -scale to scale the coordinates up to create interstices, use genconf -ci and then minimize really gently to fix all the bond lengths, and equilibrate carefully to fix the density. Mark It reports to me the inability to add any of the hydrogen molecules, ie it adds 0 molecules out of 100 requested. ###error Reading molecule configuration Gallium Rubidium Oxygen Manganese Argon Carbon Silicon Containing 3 atoms in 1 residue Initialising van der waals distances... Try 999 Added 0 molecules (out of 100 requested) of H2 Writing generated configuration to 2frv.solv.gro Back Off! I just backed up 2frv.solv.gro to ./#2frv.solv.gro.1# PERIPLASMIC HYDROGENASE; PERIPLASMIC HYDROGENASE Output configuration contains 8340 atoms in 977 residues Volume : 1299.08 (nm^3) Density : 143.043 (g/l) Number of SOL molecules: 186 Processing topology Removing line #40 'SOL 39308' from topology file (2frv.top) error end### How do i rectify this problem? I suspect the problem is due to the bond length of the hydrogen molecule that I created with 1.66A distance ( as described in my previous post) and the fact that the gap between the solvent molecules (in my case , water) is not big enough to accomodate the H2 molecules(as I had used the pdb of CO2 and replaced each O with an H and C atom
[gmx-users] Re: tutorial for ionic liquid
Hi Catarina, This file contains the parameters for MD run, e.g. timestep, number of steps, etc. Good luck with IL, Vitaly -- Vitaly V. Chaban, Ph.D. http://www-rmn.univer.kharkov.ua/chaban.html On Thu, Feb 4, 2010 at 2:39 PM, Catarina Nunes cata.nu...@gmail.com wrote: Sorry Vitaly, Can you tell me what means a file mdp? Thank you. Catarina Hello Vitaly, I have a tutorial for ionic liquids of [BMIM] [PF6] but i can´t run it 2010/2/1 Vitaly V. Chaban vvcha...@gmail.com: Dear all, Do you have any tutorial for ? Best regards Catarina I have worked with MD of RTILs quite a lot. So if you have got concrete questions, you can probably ask me directly. Vitaly V. Chaban, Ph.D. http://www-rmn.univer.kharkov.ua/chaban.html -- 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] H2 topology
On 04/02/10 21:01, 011013021-Jyotsna wrote: Dear Mark, Your suggestions were very helpful . As per the literature I am following , It is required that the dummy atom has mass 0 and charge -0.950.Hence , I created the following itp file with this in mind. ## ; topology for hydrogen. [ moleculetype ] ;name nrexcl H2 2 [ atoms ] ; nr type resnr residu atom cgnr charge mass ; total charge 1 H 1 H2 H1 1 0.475 1.00800 ; 0.00 2 H 1 H2 H2 1 0.475 1.00800 ; 0.00 3 DUM 1 H2 DUM 1 -0.950 0.0 ; 0.00 [ virtual_sites2 ] ; Site from funct a 3 1 2 1 0.074 That gets you an asymmetric dummy atom, which seems weird. David told you how to get a symmetric one. The manual also makes that clear. [ constraints ] 1 2 2 0.074 ## But during energy minimization I encountered many problems. Strictly EM is done by mdrun. Your inputs to grompp were invalid, so EM never commences. The errors are: ### error ## Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up em_ion_out.mdp to ./#em_ion_out.mdp.9# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 3 bonded neighbours molecule type 'Protein_B' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'H2' processing coordinates... double-checking input for internal consistency... Cleaning up constraints and constant bonded interactions with virtual sites renumbering atomtypes... converting bonded parameters... ERROR 1 [file 2frv_ion.top, line 40]: atom DUM (Res H2-6) has mass 0 ERROR 2 [file 2frv_ion.top, line 40]: atom DUM (Res H2-7) has mass 0 --- Program grompp_d, VERSION 4.0 Source code file: grompp.c, line: 940 Fatal error: There were 2 errors in input file(s) -- ### error Is this due to a problem in the .itp file? Yep. Dummy atoms need mass, or what is the point? Mark Even though i referred to the previous queries made in the forum , I was not able to get an answer, Please guide me as to where I have gone wrong . Thank You, jyotsna On Wed, 03 Feb 2010 22:42:09 +1100 Mark Abraham mark.abra...@anu.edu.au wrote: *This message was transferred with a trial version of CommuniGate(r) Pro* - Original Message - From: 011013021-Jyotsna 011013...@bioinfo.sastra.edu Date: Wednesday, February 3, 2010 21:48 Subject: Re: [gmx-users] H2 topology To: Discussion list for GROMACS users gmx-users@gromacs.org Dear David, Thanks for your reply. From your reply, I get the impression that the bond length of my hydrogen molecule gets adjusted duing minimization of the whole system ( protien+water+ inserted hydrogen molecule). But the issue impending is the insertion of the hydrogen molecule itself into the protein+water box created in previous step. For insertion/addition of hydrogen molecules I used the command: genbox_d -cp 2frv.conf.gro -o 2frv.solv.gro -p 2frv.top –ci h2.gro –nmol 100 What about a two-stage process? Do genbox -ci h2.gro -nmol 100 when there's no water, and then solvate *afterwards*. Or, generate solvent, and get a list of 100 random numbers in the right range, manually delete those water molecules to create interstices, update your [molecules] section, then use genconf -ci and equilibrate carefully to fix the density. Or, generate solvent for a box somewhat smaller than the one you want, use editconf -scale to scale the coordinates up to create interstices, use genconf -ci and then minimize really gently to fix all the bond lengths, and equilibrate carefully to fix the density. Mark It reports to me the inability to add any of the hydrogen molecules, ie it adds 0 molecules out of 100 requested. ###error Reading molecule configuration Gallium Rubidium Oxygen Manganese Argon Carbon Silicon Containing 3 atoms in 1 residue Initialising van der waals distances... Try 999 Added 0 molecules (out of 100 requested) of H2 Writing generated configuration to 2frv.solv.gro Back Off! I just backed up 2frv.solv.gro to ./#2frv.solv.gro.1# PERIPLASMIC HYDROGENASE; PERIPLASMIC HYDROGENASE Output configuration contains 8340 atoms in 977 residues Volume : 1299.08 (nm^3) Density : 143.043 (g/l) Number of SOL molecules: 186 Processing topology Removing line #40 'SOL 39308' from topology file (2frv.top) error end### How do i rectify this problem? I suspect the problem is due to the bond length of the hydrogen molecule that I created with 1.66A distance ( as described in my previous post) and the fact that the gap between the solvent molecules (in my case , water) is
Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial
Hi Tsjerk, Thanks for your response, I am finding problem in using original coordinates with the PRODRG topology because of mismatch in number of Hydrogen atoms in original coordinate file and PRODRG topology. Can you tell me how can I try 2nd option you suggested i.e. Fit the structure obtained from PRODRG to original structure? Thanks Regards, Vivek On 27 January 2010 10:35, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Vivek, Either 1. Use the original ligand coordinates with the PRODRG topology or 2. Fit the structure obtained from PRODRG to the original structure Cheers, Tsjerk On Wed, Jan 27, 2010 at 5:58 AM, vivek sharma viveksharma.i...@gmail.com wrote: Hi Dallas, I am trying to run MD simulation over a docked complex (protein+ligand), to confirm their dynamic stability in water media. For the same I am using PRODRG server to generate topologies for ligand molecule as gromacs can generate topology for 20 standard residues. As mentioned in tutorial for drug-enzyme complex, I am editing the .top and .gro files to include the PRODRG generated files (DRGGMX.ITP in .top and DRGAPH.GRO in .gro file). I observe that their are changes in co-ordinate of ligand after processing them through PRODRG server. So these new co-ordinates for ligand are placing ligand away from the protein while the ligand molecule was in protein pocket in original docked complex. I hope it gives what I am trying to do, and where I am getting stuck. I am looking for some suggestions and more insight of the problem to solve it. Earlier I have done same procedure successfully for a different docked complex. Regards, Vivek 2010/1/27 Dallas B. Warren dallas.war...@pharm.monash.edu.au So, what EXACTLY are you doing? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] On Behalf Of vivek sharma Sent: Monday, 25 January 2010 7:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial HI Tsjerk, Thanks for your reply. But, I can't see if it is going suddenly or gradually. What i can see is the ligand is away from the molecule after editing the gro file with PRODRG output. It seems liek PRODRG has modified the co-ordinates that places ligand away from the protein. ~Vivek 2010/1/25 Tsjerk Wassenaar tsje...@gmail.com Hi Vivek, Now when I am processing the modified .gro file to generate box, the ligand and cofactor are going away from the protein molecule and I am not able to analyze the complex. Gradually going away, or suddenly jumping? In the latter case, read up on periodic boundary conditions. Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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 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 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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial
Hi Mark, Thanks for your response, it worked well for few molecule but not for all. As I mentioned first I am doing docking and then processing receptor through pdb2gmx and ligand through PRODRG server. But number of Hydrogen atoms in docked ligand and PRODRG generated topology are not same. Although, number of Hydrogens are same in PRODRG generated topology and pdb file but I can't use them as they have modified co-ordinate than docked ligand, and the docked ligand coordinates can't be used as they dont have all Hydrogen atom as mentioned in topology file (.itp file). Can you suggest a way to come out of this problem. Thanks Regards, Vivek On 27 January 2010 10:40, Mark Abraham mark.abra...@anu.edu.au wrote: On 27/01/10 15:58, vivek sharma wrote: Hi Dallas, I am trying to run MD simulation over a docked complex (protein+ligand), to confirm their dynamic stability in water media. For the same I am using PRODRG server to generate topologies for ligand molecule as gromacs can generate topology for 20 standard residues. As mentioned in tutorial for drug-enzyme complex, I am editing the .top and .gro files to include the PRODRG generated files (DRGGMX.ITP in .top and DRGAPH.GRO in .gro file). I observe that their are changes in co-ordinate of ligand after processing them through PRODRG server. So these new co-ordinates for ligand are placing ligand away from the protein while the ligand molecule was in protein pocket in original docked complex. I hope it gives what I am trying to do, and where I am getting stuck. I am looking for some suggestions and more insight of the problem to solve it. Earlier I have done same procedure successfully for a different docked complex. So you already have the coordinate file from which you wish to begin MD, and all you need are topologies. One approach is to generate your ligand .itp file with PRODRG as above, and your protein .top file with pdb2gmx from the same coordinate file with the ligand absent. Now you can simply take the protein.top file, #include the ligand .itp file and amend the [ molecules ] section. This is now a protein+ligand .top file. Then you will need to take your original protein+ligand structure file and perhaps modify the ligand part to conform with the atom and residue names and ordering in the PRODRG output coordinate file - but you don't need to concern yourself with the coordinates it produces. As normal, you will need to take care that the coordinate file you provide to grompp has the molecules ordered in the same order of the [molecules] section, and that atoms within molecules have a corresponding ordering in .top and coordinate file. Mark -- 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 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] CHARMM TIP3-Water with GMX
Hi all I am doing some tests with the CHARMM port in GROMACS. Before to start more extensive simulations with this ff I have performed a short run of 1000 TIP3-CHARMM water molecules in a cubic during at T=300 K and P=1.015 bar with v-rescale and PR as thermostat and barostat. I have used the VERSION 4.0.99_development_20090927 of GMX. ### npt.mdp # title= Bulk TIP3 equili define= -DCHARMM_TIP3P ; CHARMM_TIP3_WATER with LJ interactions in H atoms ; Run parameters integrator= md; leap-frog integrator nsteps= 50; 2 * 50 = 1000 ps dt= 0.002; 2 fs nstcalcenergy = 5 nstcomm = 5 ; Output control nstxout= 1000; save coordinates every 2 ps nstvout= 1000; save velocities every 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; update log file every 2 ps energygrps = system ; Bond parameters continuation= yes; continuation 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; 5*2fs 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) ;vdW rvdw= 1.2; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.12; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= system; one coupling groups - more accurate tau_t= 0.1; time constant, in ps ref_t= 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl= Parrinello-Rahman ; pressure coupling in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 1.0 ; time constant, in ps ref_p = 1.0135; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, 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 ### After 1ns of MD, I can reproduce the density (1.014 g/cm3) and RDF of oxygen-oxygen water given in JCTC paper of Bjelkmar. and with g_energy_mpi -f -nmol 1000 npt.edr command I obtain Statistics over 51 steps [ 0. thru 1000. ps ], 12 data sets All averages are over 11 frames Energy Average RMSD Fluct. Tot-Drift --- LJ (SR) 4.46356 0.197047 0.196872 -0.0287239 (kJ/mol) LJ (LR) -0.0808426 0.00072743 0.000725833 0.000166929 (kJ/mol) Disper. corr. -0.109557 0.000959736 0.000957692 0.000216851 (kJ/mol) Coulomb (SR) -41.7696 0.309073 0.308661 0.0552643 (kJ/mol) Coul. recip. -3.69787 0.0144802 0.0144802 3.31364e-05 (kJ/mol) Potential -41.19430.19617 0.196016 0.0269571 (kJ/mol) Kinetic En. 7.47811 0.135378 0.135378 0.000498793 (kJ/mol) Total Energy -33.7162 0.237225 0.237093 0.027456 (kJ/mol) Temperature 299.952 5.43015.43009 0.0200087 (K) Pressure1.45811429.519429.013 -72.2231 (bar) Volume 29.4835 0.258304 0.257752 0.0584779 (nm^3) Density 1014.728.889098.87016 -2.00846 (kg/m^3) The computed RMSD of the water oxygen atoms with the command g_msd_mpi -s npt.tpr -f npt.trr -n index.ndx -b 300 -e 1000 Diffusion : D[OW] 5.3529 (+/- 0.2862) 1e-5 cm^2/s The translational diffusion are nearly corrects compared with the literature (5.86 1e-5 cm^2/s at 298 K, by Mark et Nilsson , J. Phys. Chem. A, 2001, 105 (43), pp 9954) But i noticed that my average pressure seem to high (1.5 bar) for 1ns of MD and by consequence I am not very confident with the parameters I used in my mdp. Probably this run was also to short. Moreover, since I am not a power user of GROMACS, I don't know how to translate in GROMACS directives the sentence given in JCTC paper using a short-range cutoff of 1.2 nm, and van der Waals interactions were switched off between 1.0 to 1.2 nm. And by consequence what are the corrects coulomb and vdw
[gmx-users] ice.pdbice.itp
Hello everybody, I'm Fairuz from Malaysia. I just want to ask if there is someone that have information about PDB of ice and itp file of ice. I only had PDB of the ice and trying to convert it into itp file using GAMESS software. Is there any suggestion? Thank you. -- 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] ice.pdbice.itp
fairuz zulkifli wrote: Hello everybody, I'm Fairuz from Malaysia. I just want to ask if there is someone that have information about PDB of ice and itp file of ice. I only had PDB of the ice and trying to convert it into itp file using GAMESS software. You can't. A .pdb file is a coordinate file, while an .itp is a parameter file (topology). The two are not interchangeable. I presume that you can use the parameters for water and simulate at a suitable temperature, though. -Justin Is there any suggestion? Thank you. -- 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/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] ice.pdbice.itp
fairuz zulkifli wrote: Hello everybody, I'm Fairuz from Malaysia. I just want to ask if there is someone that have information about PDB of ice and itp file of ice. I only had PDB of the ice and trying to convert it into itp file using GAMESS software. You can't. A .pdb file is a coordinate file, while an .itp is a parameter file (topology). The two are not interchangeable. I presume that you can use the parameters for water and simulate at a suitable temperature, though. -Justin Not always - that depends on what you want to study. It's very difficult to get realistic presentations of ice in MD, and the freezing temperature of water models is usually not 273K. There are some works on the subject, using an initial model prepared according to geometric specifications. I remember something from Victoria Buch but there may be newer studies around. Ran. -- 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] bonds section in the topology file
Hi, i'm simulating a surface in water and ions which is composed of 6X6 Carbon atoms arranged on a 2-d lattice. (using ffamber99) i want to keep the spacing between C-C neighbouring atoms at 0.34 Angstrom (or some other spacing of choice..), and to maintain the surface rigid and planar for that i added to the [ bonds ] section at the topology file c0 values and force constants as following: [ bonds ] ; aiaj functc0c1c2c3 1 2 1 3.40e-01 3.744680e+05 1 7 1 3.40e-01 3.744680e+05 2 3 1 3.40e-01 3.744680e+05 .. and so on.. and similarly added 90 and 180 degrees bond angle constrains between triads of atoms in the surface according to their location. the thing is , i'm affraid my constraint of c0 of 3.4 Angst. is in some conflict with the definition of C-C bond length which is defined somewhere in the amber files (if i'm turning the constraint on co off the atoms approach each other and the spacing is lost) my questions are: a) do you think i should define a new dummy atom? and in which files should it be done? - i'm asking because i didn't find a clear answer in the manual b) is there any other bond function (what number?) which may ignore the definition of the C-C length and treat only the c0 constraint? if someone can answer or guide me to relevant sections in the manual i'll be most thankful! amir -- 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] bonds section in the topology file
Amir Marcovitz wrote: Hi, i'm simulating a surface in water and ions which is composed of 6X6 Carbon atoms arranged on a 2-d lattice. (using ffamber99) i want to keep the spacing between C-C neighbouring atoms at 0.34 Angstrom (or some other spacing of choice..), and to maintain the surface rigid and planar for that i added to the [ bonds ] section at the topology file c0 values and force constants as following: [ bonds ] ; aiaj functc0c1c2c3 1 2 1 3.40e-01 3.744680e+05 1 7 1 3.40e-01 3.744680e+05 2 3 1 3.40e-01 3.744680e+05 .. and so on.. and similarly added 90 and 180 degrees bond angle constrains between triads of atoms in the surface according to their location. the thing is , i'm affraid my constraint of c0 of 3.4 Angst. is in some conflict with the definition of C-C bond length which is defined somewhere in the amber files (if i'm turning the constraint on co off the atoms approach each other and the spacing is lost) my questions are: a) do you think i should define a new dummy atom? and in which files should it be done? - i'm asking because i didn't find a clear answer in the manual b) is there any other bond function (what number?) which may ignore the definition of the C-C length and treat only the c0 constraint? Two options I can think of: 1. Why not position restrain your carbon lattices to parallel planes? 2. Use bond type 6 to define a harmonic potential between the atoms you want to restrain. If the two lattices are part of the same molecultype definition (unclear from your post), then you can use distance restraints. If they are separate molecules, however, you can't, and hence why bond type 6 is a viable option. -Justin if someone can answer or guide me to relevant sections in the manual i'll be most thankful! amir -- 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/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] extending simulation confusion?
Hi, I am trying to extend my simulation time from 100ns - 300ns. So I used the command : tpbconv -s old.tpr -extend 10 -o new.tpr but I got this: Extending remaining runtime of by 20 ps (now 14992 steps) Writing statusfile with starting step 0 and length 14992 steps... time 0.000 and length 30.000 ps So this means, basically the simulation is starting all over again and now it will run for 300ns? Is there a way I can specify what step to run from? Thanks -Nisha P -- 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] a simple doubt about g_rms
Miguel Quiliano Meza wrote: Hi everyone. Nowadays I am learning how to analyze my results after MD. I have been reading the tutorial GROMACS Tutorial for Drug – Enzyme Complex and all is fine but I have a big doubt about g_rms. I know that g_rms compares two structures by computing the root mean square deviation (RMSD). In the tutorial one part said: Use g_rms to obtain an RMSD plot of the protein backbone and the drug (IN4) throughout the simulation. Do the Backbone first g_rms –s md.tpr –f md.trr (or xtc) –o bkbone_rmsd.xvg You will be prompted to select a Group. Enter 4 (for backbone). Compare to 1 Group in the reference. Enter 1 then Enter 4 for backbone again. The last part for me is confused, I understand that I am going to compare backbone with protein so first (4) and then (1), but Enter 1 then Enter 4 for backbone again, why and what should I do if I want to calculate the RMSD of the drug? (4) and then LIG?? or (LIG) and (LIG)? The two groups serve two purposes - the first entry (per the prompt) is the group for which the least squares fit is performed. The second group (the calculation group) then has the RMSD calculated from the fitted orientations. Lots of textbooks and web resources explain the calculation in greater detail; I suggest you have a look to see what Google will offer you, as well :) -Justin I know that these are trivial questions but I would be grateful I someone can help me or give advices. Thanks in advance. Miguel. -- 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/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] extending simulation confusion?
nishap.pa...@utoronto.ca wrote: Hi, I am trying to extend my simulation time from 100ns - 300ns. So I used the command : tpbconv -s old.tpr -extend 10 -o new.tpr but I got this: Extending remaining runtime of by 20 ps (now 14992 steps) Writing statusfile with starting step 0 and length 14992 steps... time 0.000 and length 30.000 ps So this means, basically the simulation is starting all over again and now it will run for 300ns? Is there a way I can specify what step to run from? The .tpr file will always specify the entire length of the run. The point from which the simulation starts is contained in the checkpoint file. Please see here: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations -Justin Thanks -Nisha P -- 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/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] grompp in GROMACS 4
Dear all, I am new in Gromacs 4.0.7 before this I was using the GROMACS 3.3.3. I have some doubt in the grompp commands when i want to run in parallel In Gromacs 3, I just use: grompp_mpi -v -f _ _ _ -np 4 then, mdrun_mpi -v -f -deffnm -np 4 but in Gromacs 4, I cant use 4 nodes in grompp in order to prepare tpr file for 4 nodes to be used in mdrun_mpi there is no option -np in grompp and grompp_mpi Is it there is change in the command? or is due to other problems? THANKS. _ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969-- 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] grompp in GROMACS 4
edmund lee wrote: Dear all, I am new in Gromacs 4.0.7 before this I was using the GROMACS 3.3.3. I have some doubt in the grompp commands when i want to run in parallel In Gromacs 3, I just use: grompp_mpi -v -f _ _ _ -np 4 then, mdrun_mpi -v -f -deffnm -np 4 but in Gromacs 4, I cant use 4 nodes in grompp in order to prepare tpr file for 4 nodes to be used in mdrun_mpi there is no option -np in grompp and grompp_mpi Is it there is change in the command? or is due to other problems? THANKS. You posted this message already, and received two replies, one of which pointed you to a web link with a very clear solution: http://lists.gromacs.org/pipermail/gmx-users/2010-February/048593.html And you can always check the options of every command with -h, i.e.: grompp -h should give you some very obvious information. -Justin Hotmail: Free, trusted and rich email service. Get it now. https://signup.live.com/signup.aspx?id=60969 -- 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/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] bonds section in the topology file
Thank you Justin, actually, i have two parallel rigid plates that are free to move towards each other on the Y-axis (i used position restrain on Y and Z axes) later on i will umbrella sampling to obtain the plate-plate PMF at various distances from each other (thanks a lot for the helpful tutorial!) so i will try bond type 6 as you suggested. up until now i observed , especially during the the NPT run ,that the atoms are fluctuating , and if the time step was 0.002psec or even 0.001 psec the system was very un-robust and the simulation explodes. (that is my main concern and the reason for my previous post) do you think bond type 6 will settle this? anyway, thanks a lot for the quick reply! Amir On Thu, Feb 4, 2010 at 7:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: Amir Marcovitz wrote: Hi, i'm simulating a surface in water and ions which is composed of 6X6 Carbon atoms arranged on a 2-d lattice. (using ffamber99) i want to keep the spacing between C-C neighbouring atoms at 0.34 Angstrom (or some other spacing of choice..), and to maintain the surface rigid and planar for that i added to the [ bonds ] section at the topology file c0 values and force constants as following: [ bonds ] ; aiaj functc0c1c2c3 1 2 1 3.40e-01 3.744680e+05 1 7 1 3.40e-01 3.744680e+05 2 3 1 3.40e-01 3.744680e+05 .. and so on.. and similarly added 90 and 180 degrees bond angle constrains between triads of atoms in the surface according to their location. the thing is , i'm affraid my constraint of c0 of 3.4 Angst. is in some conflict with the definition of C-C bond length which is defined somewhere in the amber files (if i'm turning the constraint on co off the atoms approach each other and the spacing is lost) my questions are: a) do you think i should define a new dummy atom? and in which files should it be done? - i'm asking because i didn't find a clear answer in the manual b) is there any other bond function (what number?) which may ignore the definition of the C-C length and treat only the c0 constraint? Two options I can think of: 1. Why not position restrain your carbon lattices to parallel planes? 2. Use bond type 6 to define a harmonic potential between the atoms you want to restrain. If the two lattices are part of the same molecultype definition (unclear from your post), then you can use distance restraints. If they are separate molecules, however, you can't, and hence why bond type 6 is a viable option. -Justin if someone can answer or guide me to relevant sections in the manual i'll be most thankful! amir -- 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/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] bonds section in the topology file
Amir Marcovitz wrote: Thank you Justin, actually, i have two parallel rigid plates that are free to move towards each other on the Y-axis (i used position restrain on Y and Z axes) later on i will umbrella sampling to obtain the plate-plate PMF at various distances from each other (thanks a lot for the helpful tutorial!) so i will try bond type 6 as you suggested. up until now i observed , especially during the the NPT run ,that the atoms are fluctuating , and if the time step was 0.002psec or even 0.001 psec the system was very un-robust and the simulation explodes. (that is my main concern and the reason for my previous post) do you think bond type 6 will settle this? Not likely. If your system is blowing up that means there is something physically unrealistic about it (insufficient EM or equilibration, inappropriate parameters or .mdp settings, etc). There's tons of useful information on the Gromacs site and in the list archive to help you. Otherwise you'll have to provide substantially more information regarding all the points I raised above to get any useful advice. -Justin anyway, thanks a lot for the quick reply! Amir On Thu, Feb 4, 2010 at 7:32 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amir Marcovitz wrote: Hi, i'm simulating a surface in water and ions which is composed of 6X6 Carbon atoms arranged on a 2-d lattice. (using ffamber99) i want to keep the spacing between C-C neighbouring atoms at 0.34 Angstrom (or some other spacing of choice..), and to maintain the surface rigid and planar for that i added to the [ bonds ] section at the topology file c0 values and force constants as following: [ bonds ] ; aiaj functc0c1c2 c3 1 2 1 3.40e-01 3.744680e+05 1 7 1 3.40e-01 3.744680e+05 2 3 1 3.40e-01 3.744680e+05 .. and so on.. and similarly added 90 and 180 degrees bond angle constrains between triads of atoms in the surface according to their location. the thing is , i'm affraid my constraint of c0 of 3.4 Angst. is in some conflict with the definition of C-C bond length which is defined somewhere in the amber files (if i'm turning the constraint on co off the atoms approach each other and the spacing is lost) my questions are: a) do you think i should define a new dummy atom? and in which files should it be done? - i'm asking because i didn't find a clear answer in the manual b) is there any other bond function (what number?) which may ignore the definition of the C-C length and treat only the c0 constraint? Two options I can think of: 1. Why not position restrain your carbon lattices to parallel planes? 2. Use bond type 6 to define a harmonic potential between the atoms you want to restrain. If the two lattices are part of the same molecultype definition (unclear from your post), then you can use distance restraints. If they are separate molecules, however, you can't, and hence why bond type 6 is a viable option. -Justin if someone can answer or guide me to relevant sections in the manual i'll be most thankful! amir -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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/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
[gmx-users] ATP for
Hello gmx users, I need to use ATP's parameter for amber port in gromacs. The atp.prep and frcmod.phos for ATP can be found at http://www.pharmacy.manchester.ac.uk/bryce/amber. How can I use it in ffamber. The program amb2gmx.pl needs amber to be installed, which is not present. Same with ACPYPI. Any suggestion will be very helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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
