[gmx-users] Averege structure
I have done 15ns MD simulations at 300k temp for a protein finally obtained an average structure from g_rmsf. so please tell me is output average structure is a sampled structure? is there no need of remd or sampling further because I got plateau in RMSD calculation at last? I have strongly energy minimize by first steepest second by conjugate gradient of my protein after simulation was completed. I have got 81% residues in core region of RC plot by using this energy minimization method. I have also used SPDBv instead of former one method for EM but got 91% core region residues. Which methods should I choose to get the good model? what are the essential criteria for a good model? -- Pawan -- 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] topology builiding
Hi There, I am using x2top to build topology for a molecule using oplsaa forcefield from a pdb file. I have added a few entries in the n2t file but i have got a wrong topology as some additional bonds are made in the molecule. As far as I know x2top ignores the connect information of the atoms. Is it possible to modify the x2top code so that it reads the connect information and then build bonds . Also, if I make some changes in the x2top code, do I need to compile it the whole gromacs package again or whether I can compile it separately? Thanks, Pankhuri -- 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] charmmff
Hi, The gromacs version in git master, please see the directory share/top/charmm27.ff That directory contains whole gromacs charmm files. Furthermore, please see the reference below which explain more details about these parameters. Bjelkmar, Larsson, Cuendet, Hess, and Lindahl, JCTC 2010 I hope those informations help you. What do you want to do more specific? -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 On Tue, Jul 20, 2010 at 6:57 PM, Sai Pooja wrote: > Hi, > > If one has to make a version of gromacs charmm compatible, which files from > the charmm compatible version must be looked at? > > Pooja > > -- > Quaerendo Invenietis-Seek and you shall discover. > > -- > 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] Need For a Script
Hi Justin, I am trying to perform umbrella sampling following your link. But when I put the command grompp -f md_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o umbrella0.tpr I found the the following error No molecules were defined in the system Could you please suggest please? Samrat. From: Samrat Pal To: jalem...@vt.edu; Discussion list for GROMACS users Sent: Mon, July 19, 2010 10:00:27 AM Subject: Re: [gmx-users] Need For a Script Another thing is that I am not sure how to get the force-extension profile from the simulation trajectory? Thanks Samrat From: Samrat Pal To: jalem...@vt.edu; Discussion list for GROMACS users Sent: Sun, July 18, 2010 12:21:04 PM Subject: Re: [gmx-users] Need For a Script I have been doing the pull simulations with your scripts and that are running fine. Thanks a lot. Can I use implicit solvent model in pulling simulations? I have gone through the mailing list and I found that it is not recommended (I may be wrong). Please suggest. Thanks in advance Samrat Pal From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Fri, July 16, 2010 5:18:44 PM Subject: Re: [gmx-users] Need For a Script Samrat Pal wrote: > Dear All, > I am a new GROMACS user. I have been able to solvate a protein in a water >box and also to simulate it and unfold it by heating it. But I have facing >problem with the script of AFM pulling. I want to unfold a protein by pulling >the two ends of the protein. Can anyone give me a full script for that so that >I >can standardise my protocol? Suggestion is urgent. http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling Also, as a bit of advice, don't use the word "urgent" when asking for free help. You're hoping someone else (who is busy) will find time to solve an issue for you. -Justin >Thanks in advance > Samrat Pal > -- 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
[gmx-users] charmmff
Hi, If one has to make a version of gromacs charmm compatible, which files from the charmm compatible version must be looked at? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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] extracting coordinates
What do you want to do with the coordinates? Look-up 'trjconv' -Gaurav On Tue, Jul 20, 2010 at 11:32 AM, Vishal Agarwal wrote: > Dear All, > I am new to using GROMACS. I have done some NVT simulation on glucose > molecule. Can one anyone tell me how to extract the coordinates of atoms for > each frame from the output trajectory file. > > Thanks, > Vishal > > -- > 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] Free Energy Calculation Using Tabulated Potentials
Hi, I am having some troubles calculating free energies. Can someone please tell me if I have tabulated potentials, can I calculate free energy using the gromacs options in the mdp file for free energies. (If someone has done it, can you please provide a sample topology file.) Thanks, Nimesh -- 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] I wonder if anyone has a "gmx2lmp" tool
Hi Does anyone also use LAMMPS? I want to ask if anyone has written a tool which transfers Gromacs input files (.itp, .top, and .gro files) into a lammps ".data" input file. Thank you! Shuo Li Ph.D. Candidate in Chemical Engineering Department of Chemical & Materials Engineering University of Cincinnati Cincinnati, OH 45221 -- 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] Segmentation Fault with g_dielectric
Hello, I am trying to calculate the dielectric constant for pure tetrahydrofuran (THF) at 298K. I keep running into problems though. I have looked through the gmx user list to see if others have had these problems, but I didn't see any mention of them (although I did see that others were asked to report issues with g_dipoles to bugzilla). The first thing I do is run g_dipoles using the command (I do this in order to get the ACF to use in g_dielectric): g_dipoles -f nvt10ns.xtc -s previous.tpr -corr mol -mu 1.75 *I would have liked to attach the tpr and xtc file, but the message was too big. I can send them if they will help* When I do this, I get the following output to terminal: There are 255 molecules in the selection Using volume from topology: 34.3361 nm^3 Last Frame 3 time 12000.001 t0 0, t 12000, teller 30001 **then there is a long pause (approx 5 minutes)** Dipole Moment (Debye) __ Average = 1.9194 Std. Dev. = 0.0085 Error = 0. **Then it lists the different dipole moments, kirkwood factors, and finally an epsilon = 4.47756** (I won't bother to write all of the info down) I wanted to include the output files, but the e-mail was too big and wouldn't go through. I can send them later. It seems that the g_dipoles is working fine for me. Once I have the autocorrelation function (dipcorr.xvg), I want to use g_dielectric. Before I talk about the problems I have here, I wanted to verify a few things about the various options: epsRF - the default here is 78.5, even though the default in g_dipoles is 0 (infinity). I wanted it to be infinity, so I assume I change it. eps0 - this is the epsilon of my liquid - but is it the epsilon that was calculated from g_dipoles (4.47756)? When I run the command: g_dielectric -f dipcorr.xvg -epsRF 0 -d -o -c I get a segmentation fault before anything happens: Read data set containing 2 columns a nd 15001 rows Assuming (from data) that timestep is 0.4, nxtail = 1249 Creating standard deviation numbers ... nbegin = 13, x[nbegin] = 5.2, tbegin = 5 Segmentation Fault If I leave out the -epsRF, I still get the same error. If I include eps0, I still get a segmentation fault. It seems strange to me since GROMACS generates the input and yet has an issue with it. I would like to point out that the manual states to use dipcorr.xvg to get the dielectric constant, but after reading the paper GROMACS references, it seems that is more appropriate. I tried running the command g_dielectric -f Mtot.xvg, and the segmentation fault went away. Instead lambda went to infinity and there was a fatal error (nparm = 0 in the file ../../../../src/tools/exptfit. c, line 466. I am probably missing something obvious, but I am having a hard time figuring out what it is. I appreciate any help. Thank you for your time, Jenny -- 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] Heme_Grompp_error
Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types 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 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. This heme is bonded to MET SD and NE2 HIS as well as NA NB NC ND of heme porphyrins. It is actually these six bond which is created in topology file with pdb2gmx using specbond.dat, giving error in grompp. I tried to find these bonds in in built files of gromacs i.e. /share/top/ but I couldnt. Can any one help me and tell me where can I find these bonds/angle parameters and what should I add in ffG43a1 .itp .rtp files please help. Shahid Nayeem -- 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] extracting coordinates
Dear All, I am new to using GROMACS. I have done some NVT simulation on glucose molecule. Can one anyone tell me how to extract the coordinates of atoms for each frame from the output trajectory file. Thanks, Vishal -- 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] translation
Hi, all: I am running dynamics with PBC in xyz direction. Now I got a problem. Since PBC is applied, some atoms will move to the other side of the box and this will change the polarization. I need the results of polarization, so I do not hope that the polarization changed during the dynamics. Does anyone have idea how to solve this? Thanks in advance. Thanks, Shuangxing Dai -- 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] frezzing a bond
Justin A. Lemkul wrote: > Nilesh Dhumal wrote: >> How can I freeze a bond? > How about distance restraints instead? That raises some kind of off-topic question: In Cerius2, we use position constraints to reduce the calculation complexity, because forces between constrained atoms need not to be evaluated, this saves some simulation time. And, in our group, that's practically the only reason to do so. Now, if I recall corectly, postion and distance restraints are like stiff springs keeping the atom in a certain distance/position. Does this take more, less or the same computation time as if the bonds were free? Is it possible to use constraints in gromacs as I mentioned above? Thanks -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- 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] LINC warning but reasonable potential energy and force
Dear experts, I am trying to build up a polymer system. To do so I took a chain with 60 repeating units (ethylene) and compressed the system to attain the desired box volume (density). I took the following approach since after one week work on this problem I believe that is the only way of achieving what I want so I would like you to correct me if necessary. I know it might be a naive procedure... I noticed that in either NPT or NVT trials for a long chain equilibrium state corresponds to more extended conformations. My problem is that with this conformation I can not compress the system enough as simulation crashes (when chain takes a extended conformation that is about 2 or 3 times longer than box size applying high pressure to reduce volume causes system to explode). Hence, after performing nearly 40 NPT and NVT (and combination of these) runs I came to the point that the only way to approach the volume I am after is forget the equilibrium state (as if simulation is long chain tens to extend) and look for the globule-like structure so the volume it occupies is minimal. For instance I did a NPT for 500ps and noticed at 130 ps molecule has the convoluted structure so in the next trial I picked simul. time of 130 ps to capture the structure I want, used editconf to reduce the size, energy minimized the structure and performed the next NPT with this initial structure. Doing so, I could approach the box size of 2.3 nm (desired size is 1.8nm). Since it was not possible to compress the system further I replicated this molecule and energy minimized the replicated system. Energy minimization gives reasonable force but potential is about 3000. I dont know if this is reasonable for such a packed system. Then employed NPT to compress again to a volume a bit smaller than what I need and used editconf to attain the exact density I am after. Below is the output file of EM of the replicated and compressed system: I am getting some LINC warnings but at the end force and potential energies seem to be OK. PLease let me know if anything is going wrong. : Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 400 Step=0, Dmax= 1.0e-02 nm, Epot= 1.32635e+08 Fmax= 2.29301e+10, atom= 1004 Step=1, Dmax= 1.0e-02 nm, Epot= 2.22267e+07 Fmax= 1.39980e+09, atom= 1766 Step=2, Dmax= 1.2e-02 nm, Epot= 8.21648e+06 Fmax= 2.00629e+08, atom= 968 Step=3, Dmax= 1.4e-02 nm, Epot= 1.67342e+06 Fmax= 2.38551e+07, atom= 968 Step=4, Dmax= 1.7e-02 nm, Epot= 4.59581e+05 Fmax= 3.28726e+06, atom= 121 Step=5, Dmax= 2.1e-02 nm, Epot= 1.51948e+05 Fmax= 4.17261e+05, atom= 1766 Step=6, Dmax= 2.5e-02 nm, Epot= 4.95460e+04 Fmax= 1.64740e+05, atom= 121 Step=7, Dmax= 3.0e-02 nm, Epot= 3.20548e+04 Fmax= 8.22273e+04, atom= 968 Step=8, Dmax= 3.6e-02 nm, Epot= 2.16962e+04 Fmax= 1.86463e+04, atom= 961 Step=9, Dmax= 4.3e-02 nm, Epot= 1.29190e+04 Fmax= 3.92749e+03, atom= 1766 Step 10, time 0.02 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001238, max 0.029289 (between atoms 113 and 115) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 113114 33.60.1090 0.1103 0.1090 1765 1766 36.20.1090 0.1075 0.1090 Step= 10, Dmax= 5.2e-02 nm, Epot= 8.04986e+03 Fmax= 3.49262e+04, atom= 826 Step 11, time 0.022 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000239, max 0.008502 (between atoms 1765 and 1767) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 825826 32.20.1089 0.1096 0.1090 1765 1766 32.20.1075 0.1091 0.1090 Step= 11, Dmax= 6.2e-02 nm, Epot= 6.61167e+03 Fmax= 6.62618e+03, atom= 1766 Step 12, time 0.024 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000731, max 0.014345 (between atoms 1762 and 1765) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 825826 31.40.1096 0.1081 0.1090 1765 1766 39.60.1091 0.1076 0.1090 Step= 12, Dmax= 7.4e-02 nm, Epot= 5.16869e+03 Fmax= 9.34606e+03, atom= 1766 Step 13, time 0.026 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000966, max 0.021083 (between atoms 1765 and 1767) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 825826 46.40.1081 0.1107 0.1090 1765 1766 51.80.1076 0.1087 0.1090 Step= 13, Dmax= 8.9e-02 nm, Epot= 4.67001e+03 Fmax= 1.02723e+04, atom= 1766 Step 14, time 0.028 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001976, max 0.050316 (between atoms 1765 and 1767) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 825826 43.80.1107 0.1085 0.1090 1765 1766 92.70.1087 0.1128
[gmx-users] Re: Help needed with ACPYPI
Hi there, I didn't have time to improve opls generation in ACPYPE. I need to put a Wiki about it for the moment, but to get the Opls atomtypes, use MKTOP: http://labmm.iq.ufrj.br/mktop/ Good luck, Alan On Tue, Jul 20, 2010 at 14:42, wrote: > Hello all > > I want to study protein-ligand using OPLS ff of Gromacs. For Ligand > topology > preparation, I am using ACPYPI where I am getting "9 opls_x 1 <1> > C9__9 0.056600 0.0 ; qtot -0.253" in .itp file of ligand. > And thus, atomtype opls_x is not recognised which leads to falal error > > This C9 is of the form R1=C9H-R2 for which I also searched the > ffoplsaa.atp, > but did not get any luck. > > Hope I made myself clear.. > Any help will be highly appreciated. > -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< -- 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] Re: gmx-users Digest, Vol 75, Issue 107
. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types 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 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. This heme is bonded to MET SD and NE2 HIS as well as NA NB NC ND of heme porphyrins. It is actually these six bond which is created in topology file with pdb2gmx using specbond.dat, giving error in grompp. I tried to find these bonds in in built files of gromacs i.e. /share/top/ but I couldnt. Can any one help me and tell me where can I find these bonds/angle parameters and what should I add in ffG43a1 .itp .rtp files please help. Shahid Nayeem -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100720/9f365e5f/attachment-0001.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 75, Issue 107 ** -- 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] Re: gmx-users Digest, Vol 75, Issue 107
. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types 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 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. This heme is bonded to MET SD and NE2 HIS as well as NA NB NC ND of heme porphyrins. It is actually these six bond which is created in topology file with pdb2gmx using specbond.dat, giving error in grompp. I tried to find these bonds in in built files of gromacs i.e. /share/top/ but I couldnt. Can any one help me and tell me where can I find these bonds/angle parameters and what should I add in ffG43a1 .itp .rtp files please help. Shahid Nayeem -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100720/9f365e5f/attachment-0001.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 75, Issue 107 ** -- 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] Replica exhange - no. of processors
On 19/07/10 17:25, Sai Pooja wrote: Thanks Lanyuan. Can one use fewer processors than the number of replicas? My 0.02 £: I never did REMD, but, as far as I know, putting more processes on the same processor in any kind of parallel computing is asking for your performance to grind to a halt. On Mon, Jul 19, 2010 at 12:18 PM, Lanyuan Lu wrote: No. For GMX4 each replica can be run on multiple processors. Lanyuan On Mon, Jul 19, 2010 at 10:36 AM, Sai Pooja wrote: Hi, I would like to know if the Number_of_processors must be = Number_of_replicas? Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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
Re: [gmx-users] Tabulated potentials and performance
On 19/07/10 23:18, Lanyuan Lu wrote: From our group's experience, there is a critical point for dramatic performance drop when one uses two many tables. The possible reason is that the size of tables exceeds the cache size. However, this only happens when the number of tables is beyond something like 50. The total table size for the critical point can depend on the hardware condition. Thanks Lanyuan, good to know; 50 tables is about the order of magnitude that could come out in fact (well, it could be even 200, it depends). I would love if any developer can comment on the issue too, since it seems complicated :) m. -- 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] Potential of mean force
The tutorial to which you refer should give you all the necessary background to apply pulling to a variety of systems. In general, the procedure is the same. -Justin Quoting abdul wadood : > > Dear gmx user > > First of all I am very thankful to all of you in helping me in the running of > normal simulation using gromacs. > Now, I want to calculate pmf for enzyme ligand complex. I search for correct > direction but not found anywhere. > There is tutorial on the gromacs website but it is for peptide peptide > complex. Now, I dont understand how to specify the reference group to pull > the ligand. > The complex structure is attached. > Any kind of help in this regard will be highly appreciated. > > Many regards > > Abdul Wadood, > Research Scholar, > Dr.Panjwani Center for Molecular Medicine and > Drug Research, > International Center for Chemical and > Biological Science, > University of Karachi, Karachi-75720, Pakistan. > Email:wadoodbiochem...@hotmail.com > > > > _ > The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with > Hotmail. > http://www.windowslive.com/campaign/thenewbusy?tile=multicalendar&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_5 Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@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] Potential of mean force
Dear gmx user First of all I am very thankful to all of you in helping me in the running of normal simulation using gromacs. Now, I want to calculate pmf for enzyme ligand complex. I search for correct direction but not found anywhere. There is tutorial on the gromacs website but it is for peptide peptide complex. Now, I dont understand how to specify the reference group to pull the ligand. The complex structure is attached. Any kind of help in this regard will be highly appreciated. Many regards Abdul Wadood, Research Scholar, Dr.Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Science, University of Karachi, Karachi-75720, Pakistan. Email:wadoodbiochem...@hotmail.com _ The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multicalendar&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_5-- 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] Help needed with ACPYPI
Hello all I want to study protein-ligand using OPLS ff of Gromacs. For Ligand topology preparation, I am using ACPYPI where I am getting "9 opls_x 1 <1> C9__9 0.056600 0.0 ; qtot -0.253" in .itp file of ligand. And thus, atomtype opls_x is not recognised which leads to falal error This C9 is of the form R1=C9H-R2 for which I also searched the ffoplsaa.atp, but did not get any luck. Hope I made myself clear.. Any help will be highly appreciated. -- -- SUNITA GUPTA -- 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
