[gmx-users] mean square displacement
Hello all I would like to plot mean square displacement of hydrogen atoms of protein versus temperature (in order to get dynamical transition temperature). I am using g_msd for this purpose (g_msd -f *_nopbc.xtc -s *.tpr -n index.ndx -o *.xvg) . I am getting following curves as uploded in : http://s903.photobucket.com/user/nidhikatyal1989/media/msd_fig1_zpsc293a5ab.jpg.html How should I plot msd value versus temperature? Is it reasonable enough to take average over 2 ns (linear part) and discard the rest? Moreover, I suspect there is something wrong in the curves too since they are increasing first, reaching saturation and again increasing (last part is unexpected). Actually I am trying to reproduce the results of following paper: THE JOURNAL OF CHEMICAL PHYSICS 130, 135101 2009, FIG 9 (a) My values are also deviating by larger amount. Am I doing something wrong? Please help. Thanks Nidhi -- 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] regarding MSD
Please reply. Reposting the same query again: I have read few papers that determine transition temperature from the plot of average MSD of hydrogen atoms of protein versus temperature. My question is: At a particular temperature, we get a linear curve for MSD versus time, is it reasonable to calculate average MSD over all such time points? Is this the average that is plotted in papers (or something is missing) ? My doubt is won't this average depend on the number of time points (due to its linear nature)? Actually I am trying to reproduce the results of some published data. Although I am getting the same transition temperature but the MSD values are coming different (eg at a particular temperature if I average all the MSD values, I am getting value of 15000 while reported value is 1.5 - both values in same unit angstrom square) On Fri, Aug 22, 2014 at 7:15 PM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: -- Forwarded message -- From: Nidhi Katyal nidhikatyal1...@gmail.com Date: Fri, Aug 22, 2014 at 11:41 AM Subject: Re: regarding MSD To: Discussion list for GROMACS users gmx-us...@gromacs.org Hello I have posted the query earlier but havent got any reply and so reposting it again. I have read few papers that determine transition temperature from the plot of average MSD of hydrogen atoms of protein versus temperature. My question is: At a particular temperature, we get a linear curve for MSD versus time, is it reasonable to calculate average MSD over all such time points? Is this the average that is plotted in papers (or something is missing) ? My doubt is won't this average depend on the number of time points (due to its linear nature)? Actually I am trying to reproduce the results of some published data. Although I am getting the same transition temperature but the MSD values are coming different (eg at a particular temperature if I average all the MSD values, I am getting value of 15000 while reported value is 1.5 - both values in same unit angstrom square) Any help is highly appreciated. On Thu, Aug 21, 2014 at 9:56 PM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Hello all I have read few papers that determine transition temperature from the plot of average MSD versus temperature. My question is: At a particular temperature, we get a linear curve for MSD versus time, is it reasonable to calculate average MSD over all such time points? Is this the average that is plotted in papers (or something is missing) ? My doubt is won't this average depend on the number of time points (due to its linear nature)? Any help is highly appreciated. Thanks Nidhi -- 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] regarding MSD
Hello I have posted the query earlier but havent got any reply and so reposting it again. I have read few papers that determine transition temperature from the plot of average MSD of hydrogen atoms of protein versus temperature. My question is: At a particular temperature, we get a linear curve for MSD versus time, is it reasonable to calculate average MSD over all such time points? Is this the average that is plotted in papers (or something is missing) ? My doubt is won't this average depend on the number of time points (due to its linear nature)? Actually I am trying to reproduce the results of some published data. Although I am getting the same transition temperature but the MSD values are coming different (eg at a particular temperature if I average all the MSD values, I am getting value of 15000 while reported value is 1.5 - both values in same unit angstrom square) Any help is highly appreciated. On Thu, Aug 21, 2014 at 9:56 PM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Hello all I have read few papers that determine transition temperature from the plot of average MSD versus temperature. My question is: At a particular temperature, we get a linear curve for MSD versus time, is it reasonable to calculate average MSD over all such time points? Is this the average that is plotted in papers (or something is missing) ? My doubt is won't this average depend on the number of time points (due to its linear nature)? Any help is highly appreciated. Thanks Nidhi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] regarding g_hydorder
Hello all I would like to calculate both distance and angle water orientational order. I have made an index file containing all oxygen atoms of water and used trjorder as: g_hydorder -f *.xtc -s *.tpr -n *.ndx -o file1_1 file2_1 -or file1_2 file2_2 How to interpret the results of the output files? Both output files file1_2 and file2_2 contain the same content. Won't one should contain distance and other angle orientational order parameter values? Also I expect parameter values to be less than or equal to 1. But the values in the file looks something like the following (all greater than 1): #Legend #TBlock #Xbin Ybin Z t 0 0 0 6.5 0 1 6.5 0 2 4.5 0 3 3.5 0 4 6.5 0 5 4.5 0 6 5.5 1 0 6.5 1 1 4.5 1 2 5.5 1 3 3.5 1 4 5.5 1 5 4.5 1 6 5.5 2 0 4.5 . . Please help me in interpreting this file. Thanks Nidhi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] regarding MSD
Hello all I have read few papers that determine transition temperature from the plot of average MSD versus temperature. My question is: At a particular temperature, we get a linear curve for MSD versus time, is it reasonable to calculate average MSD over all such time points? Is this the average that is plotted in papers (or something is missing) ? My doubt is won't this average depend on the number of time points (due to its linear nature)? Any help is highly appreciated. Thanks Nidhi -- 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] atoms are not part of any of the T-Coupling groups
gmxcheck of my index file gives: Contents of index file index.ndx -- Nr. Group #Entries FirstLast 0 System 2230 12230 1 Protein 2226 12226 2 Protein-H 2226 12226 3 C-alpha 308 32218 4 Backbone 922 12219 5 MainChain 1232 12226 6 MainChain+Cb1488 12226 7 MainChain+H 1232 12226 8 SideChain994 82225 9 SideChain-H 994 82225 10 Prot-Masses 2226 12226 11 non-Protein422272230 12 Ion422272230 13 CU 222272229 14 ZN 222282230 15 r_131__chA8 956 963 16 r_131__chB820692076 17 r_132 1112071217 18 r_286 1126112621 19 CA_chA_r131112091209 20 CA_chB_r131126132613 and following are the contents of my .mdp file: title = Umbrella pulling simulation define = -DPOSRES_CA_chA_r131 ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= Y N N pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = CA_chA_r131 pull_group1 = CA_chB_r131 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 4200 ; kJ mol^-1 nm^-2 Thanks in advance. Nidhi On Wed, Aug 6, 2014 at 8:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/6/14, 3:46 AM, Nidhi Katyal wrote: Hello all, I am working on protein with two chains. I would like to restrain one atom of one chain while doing steered MD. For the same reason, I have created an index file that includes that atom, then created its posre.itp file and finally included following lines at the end of topol_Protein_chainA.itp: ; Include Position restraint file #ifdef POSRES_CA_chA_r131 #include posre.itp #endif I am also pasting a small section of my topol.top file: ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp #include topol_Ion_chain_A2.itp #include topol_Ion_chain_B2.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif After carrying out NPT equilibration, when I run following command: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr as given in tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/umbrella/05_pull.html I am getting following error: 215400 atoms are not part of any of the T-Coupling groups Since my pull.mdp file as the same as given in tutorial, my coupling groups are Protein and Non-Protein. I suspect there is something wrong while adding restraints using include file mechanism. Please help me resolve the problem. The error is not a result of the #include mechanism; it's a problem in the group definitions, either in the .mdp file or in the index file. Without the full text of the .mdp and the gmxcheck output of the index.ndx file, there's little to suggest. -Justin
[gmx-users] atoms are not part of any of the T-Coupling groups
Hello all, I am working on protein with two chains. I would like to restrain one atom of one chain while doing steered MD. For the same reason, I have created an index file that includes that atom, then created its posre.itp file and finally included following lines at the end of topol_Protein_chainA.itp: ; Include Position restraint file #ifdef POSRES_CA_chA_r131 #include posre.itp #endif I am also pasting a small section of my topol.top file: ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp #include topol_Ion_chain_A2.itp #include topol_Ion_chain_B2.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif After carrying out NPT equilibration, when I run following command: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr as given in tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html I am getting following error: 215400 atoms are not part of any of the T-Coupling groups Since my pull.mdp file as the same as given in tutorial, my coupling groups are Protein and Non-Protein. I suspect there is something wrong while adding restraints using include file mechanism. Please help me resolve the problem. Thanks Nidhi -- 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] Groups in index.ndx
Use make_ndx -f *.gro -n old_index.ndx -o old_index.ndx On Fri, Jul 25, 2014 at 4:53 PM, INPE (Ingrid Viveka Pettersson) i...@novonordisk.com wrote: Dear Group, I have defined different specific groups in the index.ndx file. My problem is that if I try to add a new group, the old ones are disappearing. Should it be like this? Yours sincerely, Ingrid Pettersson _ Ingrid Pettersson, PhD Principal Scientist Diabetes Structural Biology Novo Nordisk A/S Novo Nordisk Park DK-2760 Måløv Denmark +4530754506 (direct) i...@novonordisk.com Facebookhttp://www.facebook.com/novonordisk | Twitter http://www.twitter.com/novonordisk | LinkedIn http://www.linkedin.com/company/novo-nordisk | Youtube http://www.Youtube.com/novonordisk | Pinterest http://www.pinterest.com/novonordisk This e-mail (including any attachments) is intended for the addressee(s) stated above only and may contain confidential information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information contained herein is strictly prohibited and may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete it immediately hereafter. Thank you. -- 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] Running job on GPUs
Hello all I am trying to run my job on 2 nodes by utilizing all available cores. On each node of the cluster, we have two GPUs and two sockets with 8 cores each. Every time I am submitting the job, we find that it is running on one node. How to make use of the other node? Till now, I have used following trial commands as suggested in http://www.gromacs.org/Documentation/Acceleration_and_parallelization 1) mpirun -n 2 mdrun_mpi -v -deffnm nvt -ntomp 16 output: Using 2 MPI processes Using 16 OpenMP threads per MPI process WARNING: Oversubscribing the available 16 logical CPU cores with 32 threads. This will cause considerable performance loss! 2) mpirun -n 4 mdrun_mpi -v -deffnm nvt -ntomp 8 output: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 4 PP MPI processes per node, but only 2 GPUs were detected. I understand that the above error comes when number of MPI ranks is not a multiple of number of GPUs intended to be used. But in my case 4 is a multiple of 2. 3) mpirun -n 4 -npernode 2 mdrun_mpi -v -deffnm nvt The job still runs on 1 node. How can I run my job on 2 nodes utilizing all cores and GPUs? Thanks Nidhi -- 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] g_hbond
Hi all, I have created hydrogen bond existence map. In the index file generated using hbn option I can see following lines at the end: 1 2 1598 1 2 1851 1 2 1852 1 2 1862 10 11 1643 10 11 1651 10 11 1658 10 11 1664 10 11 1682 10 11 1748 10 11 1754 10 11 1761 10 11 1762 10 11 1772 10 11 1830 10 11 1831 10 11 1838 10 11 1851 10 11 1862 There are 19 lines in total and also in the existence map created using hbm option, I could see 19 lines. But when I generate index file with a2 and calculate hydrogen bond with my ligand moleules, I can see zero bonds. Am I doing something wrong? Thanks Nidhi -- 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] Hydrogen bond existence map
Hi all I would like to create hydrogen bond existence map for interaction of each residue with my ligand. I am aware that -hbm and -hbn option of g_hbond along with index file would serve the purpose. But the resulting output file is giving existence map for each atom of the residue. Instead, I want one map for residue as a whole. Example if any residue of protein is forming hydrogen bond with my ligand for certain time through bond A but for the remaining time it forms through bond B, then I want the map to show presence of hydrogen bond through one single line during the entire course of simulation. Is it possible with gromacs? Thanks in advance Nidhi -- 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] binding sites with MD
Hi all, I would like to ask if unbiased MD in nanoseconds time scale be used to find the potential binding sites of ligand with protein? I have simulated for 50ns, 1:14 and 1:24 protein:ligand simultaneously with random placement of ligand initially. In the time interval between 40 to 50ns, movement of ligand molecules can be seen around certain sites only for both the runs. Can these sites be considered as binding sites? Also, ligand molecules are involved in both hydrophobic and hydrogen bonding interactions with these sites. Thanks in advance. -- 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] parameters problem
Thanks Mark. Yes, my ligand.itp indeed has both [atomtypes] entry as well as [molecule] entry. I have followed the following procedure to #include while creating my first molecule: Run pdb2gmx command. Added #include ligand.itp after #include charmm27.ff/forcefield.itp but before [ moleculetype ] ; Namenrexcl Protein_chain_A 3 and added at the end: [ molecules ] ; Compound#mols Protein_chain_A 1 LIG 1 SOL 17063 then I have merged protein and ligand coordinates by inserting ATOM lines from ligand.pdb to *.pdb generated after pdb2gmx command. Then. I run editconf, genbox and finally grompp command. After which I got following error: Fatal error: No such moleculetype LIG My both *.itp and *.pdb files contains LIG. How to rectify the error? Thanks in advance. On Tue, Mar 11, 2014 at 1:39 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Probably you will see that your ligand.itp has an [atomtypes] entry as well as a [molecule] entry, and the former cannot follow any instance of the latter. Such an .itp file must be #included to create the first molecule. You have your protein [molecule] above the #include ligand.itp at the moment, which would cause this problem. Mark On Mon, Mar 10, 2014 at 7:09 PM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: To test swiss param parameters, I have generated *.pdb and *.itp files from it. In the genbox command, I have used -ci *.pdb -nmol 2. I have included *.itp in the topology as: ; Include Position restraint file ;#ifdef POSRES ;#include posre.itp ;#endif ;Include ligand topology #include ligand.itp ; Include water topology #include charmm27.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include charmm27.ff/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 LIG 2 SOL 12904 But after I run grompp command, I get following error: Fatal error: Syntax error - File ligand.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Please help me rectify the problem of the order getting violated although same worked for topology generated by PRODRG. Thanks in advance. On Mon, Mar 10, 2014 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/10/14, 8:21 AM, Nidhi Katyal wrote: Thanks Justin. I would also like to know the reliability of parameters generated using swiss param. I have no personal experience with it. My rule is to never trust anything from a black-box server without verifying it and assessing any information about penalties, deviations, etc. that it provides. -Justin On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/10/14, 2:45 AM, Nidhi Katyal wrote: Thank you Mark and Justin. Now, I have carried out simulations using PME electrostatics and using all other parameters (except gromos 96 43a1 ff used) as suggested in http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/lysozyme/ The protein is not loosing its structure now. But the problem is if I carry out simulations in the presence of experimentally known stabiliser generated using ProDrg (keeping all the parameters same while simulating both in the presence and absence of stabiliser), the partial loss of secondary structure is observed in the presence of stabilizer relative to the case in its absence at 350K thereby implying simulations going against experimental observations (although slight stabilization was observed at 300K). Simulations were repeated twice with two different force fields. However if I use above em,pr,full parameters with cut-off electrostatics, although secondary structure is lost in the initial stages but I could clearly see the stabilization behaviour of additive in terms of secondary structure retainment till longer time. Is this observation a matter of chance- reliable or not? What could be the possible reason for not observing such stabilization with better parameters? Cutoff electrostatics are horribly inaccurate. The fact that you conveniently see what you hope to when using a plain cutoff is likely by chance. The bigger issue is the use of PRODRG parameters. As I have said numerous times on this list, the parameters it produces are demonstrably inaccurate and require reparametrization. http://pubs.acs.org/doi/abs/10.1021/ci100335w -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA
Re: [gmx-users] parameters problem
To test swiss param parameters, I have generated *.pdb and *.itp files from it. In the genbox command, I have used -ci *.pdb -nmol 2. I have included *.itp in the topology as: ; Include Position restraint file ;#ifdef POSRES ;#include posre.itp ;#endif ;Include ligand topology #include ligand.itp ; Include water topology #include charmm27.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include charmm27.ff/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 LIG 2 SOL 12904 But after I run grompp command, I get following error: Fatal error: Syntax error - File ligand.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Please help me rectify the problem of the order getting violated although same worked for topology generated by PRODRG. Thanks in advance. On Mon, Mar 10, 2014 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/10/14, 8:21 AM, Nidhi Katyal wrote: Thanks Justin. I would also like to know the reliability of parameters generated using swiss param. I have no personal experience with it. My rule is to never trust anything from a black-box server without verifying it and assessing any information about penalties, deviations, etc. that it provides. -Justin On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/10/14, 2:45 AM, Nidhi Katyal wrote: Thank you Mark and Justin. Now, I have carried out simulations using PME electrostatics and using all other parameters (except gromos 96 43a1 ff used) as suggested in http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/lysozyme/ The protein is not loosing its structure now. But the problem is if I carry out simulations in the presence of experimentally known stabiliser generated using ProDrg (keeping all the parameters same while simulating both in the presence and absence of stabiliser), the partial loss of secondary structure is observed in the presence of stabilizer relative to the case in its absence at 350K thereby implying simulations going against experimental observations (although slight stabilization was observed at 300K). Simulations were repeated twice with two different force fields. However if I use above em,pr,full parameters with cut-off electrostatics, although secondary structure is lost in the initial stages but I could clearly see the stabilization behaviour of additive in terms of secondary structure retainment till longer time. Is this observation a matter of chance- reliable or not? What could be the possible reason for not observing such stabilization with better parameters? Cutoff electrostatics are horribly inaccurate. The fact that you conveniently see what you hope to when using a plain cutoff is likely by chance. The bigger issue is the use of PRODRG parameters. As I have said numerous times on this list, the parameters it produces are demonstrably inaccurate and require reparametrization. http://pubs.acs.org/doi/abs/10.1021/ci100335w -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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
[gmx-users] antiparallel beta sheet
Dear users, I would like to analyse the time variation of antiparallel beta sheet formation. I am aware that dssp and stride program can calculate the beta sheet content but is there a tool that can distinguish between antiparallel and parallel beta sheet (in terms of giving numeric value as output and not through visual inspection)? Thanks in advance. Nidhi -- 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] xpm2ps
Hello, I would like to change the scale of x axis and y axis of my dssp.eps file by different amounts. Example with xpm2ps -skip command I can write out every nr-th row and nr-th column but I want every nr-th row and mr-th column. Please suggest if it is possible to do so. Thanks in advance. Nidhi -- 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] parameters problem
Dear all I am trying to simulate a protein in 3 steps: energy minimization (using em.mdp), position restraints (using pr.mdp) and final production run by NPT ensemble (using full.mdp) at 300K At this temperature, it is known by previous literature survey that protein keeps its secondary structure almost intact. But according to my simulations (done thrice), protein starts loosing its secondary structure around 6-8ns only. I have used the following parameters: *em.mdp* ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 25 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.001 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no *pr.mdp* ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 5 ; total 100 ps. nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = ProteinNon-protein tau_t = 0.10.1 ref_t = 300300 ; Energy monitoring energygrps = ProteinNon-protein ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 *full.mdp* ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 2500 ; total 5 ps. nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-protein tau_t = 0.10.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-protein ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 I don't think it is the problem of thermostat because even after using V-rescale for temperature coupling and Parinello Rahman for pressure coupling, my protein loses its secondary structure in the initial time of simulation. Also, I have carried out various checks (like potential energy convergence after em, temperature check after pr, and pressure and density check after full), all of which seems to converge well. Please help me figure out the problem. -- 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.
