[gmx-users] Re:Re:Why REMD simulation becomes so slow when the number of replicas becomes large?
Hi Mark, Your analyses are quite reasonable. The low-temperature replicas are indeed doing much more work than the high-temperature replicas. As you said, the lowest temperature replica in the 24-replica should take an amount of time comparable to that of the lowest in the 42-replica. So for my case, the load imbalance across replicas is only partly to blame. Now I can exclude factors from the REMD parameters themselves. I will ask the system admin for possible explanations. May I ask when you do REMD with NVT ensemble, is it right that all your replicas are running with the same Volume as the lowest-temperature replica? Or do you equilibrate each replica with NPT ensemble, then NVT ensemble, and then feed the equilibrated structures to NVT REMD simulations? Thank you for all your helpful suggestions! Qiong Hi Mark, Many thanks for your fast response! What's the network hardware? Can other machine load influence your network performance? The supercomputer system is based on the Cray Gemini interconnect technology. I suppose this is a fast network hardware... Are the systems in the NVT ensemble? Use diff to check the .mdp files differ only how you think they do. The systems are in NPT ensemble. I saw some discussions on the mailing list that NPT ensemble is superior to NVT ensemble for REMD. And the .mdp files differ only in the temperature. Maybe so, but under NPT the density varies with T, and so with replica. This means the size of neighbour lists varies, and the cost of the computation (PME or not) varies. The generalized ensemble is limited by the progress of the slowest replica. If using PME, in theory, you can juggle the contribution of the various terms to balance the computation load across the replicas, but this is not easy to do. What are the values of nstlist and nstcalcenergy? Previously, nstlist=5, nstcalcenergy=1 Thank you for pointing this out. I checked the manual again that this option affects the performance in parallel simulations because calculating energies requires global communication between all processes. So I have set this option to -1 this time. This should be one reason for the low parallel efficiency. And after I changed nstcalcenergy=-1, I found there was a 3% improvement on the efficiency compared with those when nstcalcenergy=1. Yep. nstpcouple and nsttcouple also influence this. Take a look at the execution time breakdown at the end of the .log files, and do so for more than one replica. With the current implementation, every simulation has to synchronize and communicate every handful of steps, which means that large scale parallelism won't work efficiently unless you have fast network hardware that is dedicated to your job. This effect shows up in the Rest row of the time breakdown. With Infiniband, I'd expect you should only be losing about 10% of the run time total. The 30-fold loss you have upon going from 24-42 replicas keeping 4 CPUs/replica suggests some other contribution, however. I checked the time breakdown in the log files for short REMD simulations. For the REMD simulaiton with 168 cores for 42 replicas, as you see below, the “Rest” makes up as surprisingly high as 96.6% of the time for one of the replicas. This parameter is almost the same level for the other replicas. For the REMD simulation with 96 cores for 24 replicas, the “Rest” takes up about
[gmx-users] Increasing machine precision
Hello, Is there a way to continue minimizing after reaching machine precision? Emtol and the number of iterations are sufficient to continue. I am assuming that reaching machine precision means that the gradient of change from one iteration to another has become so small that further minimization will not improve the structure. Is this correct? If so is it possible to change the cut-off point for this gradient? Thank you in advance, have a nice day, Abdullah -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Increasing machine precision
Hello, Is there a way to continue minimizing after reaching machine precision? Emtol and the number of iterations are sufficient to continue. I am assuming that reaching machine precision means that the gradient of change from one iteration to another has become so small that further minimization will not improve the structure. Is this correct? If so is it possible to change the cut-off point for this gradient? Thank you in advance, have a nice day, Abdullah The machine precision is the limit where the computer can't add a small number (e.g. the gradient) to a larger number (e.g. the coordinates). You could try using double precision, where your computer uses twice the number of bits to store the floating point numbers. I wouldn't bother doing that though, because the energy minimization is normally just used to releave structural strain from your system so that your md simulation won't crash due to enormous forces. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: No residue type for 'ARG' as a starting terminus
Hi all, I am getting following during while running pdb2gmx for a RNA moleculei am using amber99sb force field parameters The details of the error is as: Fatal error: In the chosen force field there is no residue type for 'ARG' as a starting terminus For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- * --- Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] OPLS and RB parameters in GROMACS
Hi all, Hi I've converted the OPLS-AA torsional potential parameters for the alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation), C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found that the calculated values are different. A previous post to the gmx-users mailing list on March 27, 2008, pointed out this issue for the H-C-C-H torsional potential but there was no response to that. Does anyone know if there is an error in the ffoplsaabon.itp file? Or is there a newer set of OPLS-AA parameters? For the OPLS-AA parameters (in kcal/mol), I used: dihedral V1 V2 V3 C-C-C-C1.740 -0.157 0.279 C-C-C-H 0.0 0.00.366 H-C-C-H 0.0 0.00.318 from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as: dihedral C0 C1 C2 C3 C-C-C-C3.56686 -1.889076 0.65688 -2.33467 C-C-C-H 0.66526 1.99577 0.0 -2.661024 H-C-C-H 0.76567 -2.297020.0 -3.06269 the parameters in the ffoplsaabon.itp file are: dihedral C0 C1 C2 C3 C-C-C-C 2.9288 -1.4644 0.2092 -1.6736 C-C-C-H 0.6276 1.882800.0 -2.5104 H-C-C-H 0.6276 1.8828 0.0 -2.5104 Thankyou for any clarification. Sulatha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re:gmx-users Digest, Vol 82, Issue 56
Hi,guys I obtained surface tension of water and salt solution. But the value RMSD was always very big although the value of 65 is reasonable. Is it all right about the RMSD?? Energy Average Err.Est. RMSD Tot-Drift --- Total Energy-137595 13373.628 -80.3863 (kJ/mol) Temperature 300.019 0.0243.77499 0.100291 (K) #Surf*SurfTen 1285.17 161930.44 -127.147 (bar nm) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] sufrace tension RMSD too big
Hi,guys I obtained surface tension of water and salt solution. But the value RMSD was always very big although the value of 65 is reasonable. Is it all right about the RMSD?? Energy Average Err.Est. RMSD Tot-Drift --- Total Energy-137595 13373.628 -80.3863 (kJ/mol) Temperature 300.019 0.0243.77499 0.100291 (K) #Surf*SurfTen 1285.17 161930.44 -127.147 (bar nm) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] OPLS and RB parameters in GROMACS
There is no error. The alkane dihedral parameters were updated in 1999, and differ from those originally published in 1996. Andrew On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S mssula...@gmail.com wrote: Hi all, Hi I've converted the OPLS-AA torsional potential parameters for the alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation), C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found that the calculated values are different. A previous post to the gmx-users mailing list on March 27, 2008, pointed out this issue for the H-C-C-H torsional potential but there was no response to that. Does anyone know if there is an error in the ffoplsaabon.itp file? Or is there a newer set of OPLS-AA parameters? For the OPLS-AA parameters (in kcal/mol), I used: dihedral V1 V2 V3 C-C-C-C1.740 -0.157 0.279 C-C-C-H 0.0 0.00.366 H-C-C-H 0.0 0.00.318 from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as: dihedral C0 C1 C2 C3 C-C-C-C3.56686 -1.889076 0.65688 -2.33467 C-C-C-H 0.66526 1.99577 0.0 -2.661024 H-C-C-H 0.76567 -2.297020.0 -3.06269 the parameters in the ffoplsaabon.itp file are: dihedral C0 C1 C2 C3 C-C-C-C 2.9288 -1.4644 0.2092 -1.6736 C-C-C-H 0.6276 1.882800.0 -2.5104 H-C-C-H 0.6276 1.8828 0.0 -2.5104 Thankyou for any clarification. Sulatha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Reduced Units
Dear all I would like to do coarse-grained simulations using reduced LJ units. As I can see in the manual, this is possible, but I don't understand how... I use the Gromos96 53a6 force field. In the *ffG53a6nb.itp *the* σ* and *ε* are in *(nm*) and *(KJ/mol*) Also in the *ffG53a6.atp* the *mas*s is in* gr/mol*. Finally in the *mdp*file the *ref_t* is in *(K)* and the *time_step* in *(ps)* If I creat an atom A, and define *ε=σ=m=1*, how can I define that I want these numbers to be in reduced units? Also, how can I have reduced units in my *.mdp *file? Kind Regards, Chrysostomos -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: free energy calculation , grompp crash
hello Now it is almost clear what happened. When couple-intramol is no (default), all pairwise vdm and charge interaction becomes bonded interaction. All intra-molecular non-bonded interactions for moleculetype couple-moltype are replaced by exclusions and explicit pair interactions. In this manner the decoupled state of the molecule corresponds to the proper vacuum state without periodicity effects. But there is still one thing I don't fully understand. Mdrun will complain Warning: 1-4 interaction between 1 and 114 at distance 2.035 which is larger than the 1-4 table size 2.000 nm. I guess is that every pair wiii have 1-4 interaction because every pair (except exclusion) becomes bonded interaction. These fake 1-4 are not calculated as an 1-4 interaction so that I can neglect this warning, right? thanks. dawei -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Nice Present
This was very useful for me http://www.sunsetstripbillboards.com/info.html Wanna share with you. -- Boaz Kan-Tor I am a humanist, which means, in part, that I have tried to behave decently without expectations of rewards or punishments after I am dead. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ask for help on MARTINI SIMULATION OF POPC lipids with polarisable water
Dear All, I have performed a simulation of POPC with polarisable water model in presence of 0.2 mol CaCl2 based on MARTINI CG model. I used shift for the electrostatic interactions and the job was done on a 8-core node with domain decomposition 2 2 2. The lipid bilayer consists of 512 lipid and 16000 water. However, the simulation crashed after about 100 ns. The error message is given by: DD step 5103999 load imb.: force 5.1% Step Time Lambda 5104000 102080.00.0 Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Potential 1.18271e+046.29597e+04 -4.34519e+05 -3.22701e+05 -6.82433e+05 Kinetic En. Total EnergyTemperature Pressure (bar) Cons. rmsd () 1.66874e+05 -5.15560e+053.10498e+021.50257e+011.85079e-04 Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: G96Angle of 19936 missing 1 Molecule type 'POPC' the first 10 missing interactions, except for exclusions: G96Angle atoms456 global 3696 3697 3698 --- Program mdrun_s_mpi, VERSION 4.0.7 Source code file: domdec_top.c, line: 341 Fatal error: 1 of the 56736 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck I turned on PME for testing, but it crashed within 1 ns. Could somebody give me some suggestion on how to solve this problem? Thanks! Wei Zhao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Help with B2AR within the POPC membrane
Dear gmxusers, I need to perform molecular dynamics simulation of a B2AR within the POPC membrane. I have downloaded the 128b.pdb, popc.itp and lipid.itp files from Prof.Tieleman's group. My protein of interest is 343 residues. Also, I aligned the protein and membrane. I followed the Justin Lemkul tutorial for KALP-15. The result of inflate.gro is in agreement with the result showed in the tutorial (Visual inspection with VMD). However, the result of the first minimization shows that the protein and lipids are separated rather than starting to pack. I'm using gromacs-4.5.3. Can someone help me? my minim.mdp file: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save define = -DSTRONG_POSRES ; position restrain the protein integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; Short-range electrostatic cut-off rvdw= 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) Best regards, Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx; aldoseg...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help with B2AR within the POPC membrane
Aldo Segura wrote: Dear gmxusers, I need to perform molecular dynamics simulation of a B2AR within the POPC membrane. I have downloaded the 128b.pdb, popc.itp and lipid.itp files from Prof.Tieleman's group. My protein of interest is 343 residues. Also, I aligned the protein and membrane. I followed the Justin Lemkul tutorial for KALP-15. The result of inflate.gro is in agreement with the result showed in the tutorial (Visual inspection with VMD). However, the result of the first minimization shows that the protein and lipids are separated rather than starting to pack. I'm using gromacs-4.5.3. Can someone help me? Energy minimization does not pack the lipids around the protein. You have to do numerous iterations of shrinking + EM to accomplish this. There is a protocol in the tutorial for this. Or is there some other problem? -Justin my minim.mdp file: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save define = -DSTRONG_POSRES ; position restrain the protein integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; Short-range electrostatic cut-off rvdw= 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) Best regards, Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx; aldoseg...@gmail.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help with B2AR within the POPC membrane
Thanks for your answer. You're right in the procedure for the packing of the protein and lipids. However, after several iterations (~30) the lipids are packaged to form the bilayer and the protein is outside of it. I can send you a couple of pictures for a better explanation of my problem. Best regards, Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx; aldoseg...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help with B2AR within the POPC membrane
Aldo Segura wrote: Thanks for your answer. You're right in the procedure for the packing of the protein and lipids. However, after several iterations (~30) the lipids are packaged to form the bilayer and the protein is outside of it. I can send you a couple of pictures for a better explanation of my problem. That typically happens when either (1) the box vectors are not set correctly during system construction or (2) the protein is not properly positioned in the box. -Justin Best regards, Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx; aldoseg...@gmail.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help with B2AR within the POPC membrane
Dear Justin, You're right, I corrected the box vectors , and it works! Thanks, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: g_rmsf
Hi, I want to calculate the RMSF of residues and not of protein ... how can this be done with g_rmsf.. Also I want to see the rmsf of certain residues .. for which I created the .ndx file containint those residues only .. and after using g_rmsf with index file gives the RMSF for whole protein backbone and not for that index file residues ... what shall I do to have RMSF of index file residues ?? -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_rmsf
bharat gupta wrote: Hi, I want to calculate the RMSF of residues and not of protein ... how can this be done with g_rmsf.. Also I want to see the rmsf of certain residues .. for which I created the .ndx file containint those residues only .. and after using g_rmsf with index file gives the RMSF for whole protein backbone and not for that index file residues ... what shall I do to have RMSF of index file residues ?? The default output of g_rmsf is a plot of RMSF (of each residue) vs. residue. No index file is required to obtain this, unless you want to do the fitting to some custom group. Is this not what you want? -Justin -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_rmsf
Actually after loop incorporation I want to check which region of the protein shows much deviation , which I think can be done by plotting rmsf values from both proteins.. but the problem here is that one structure which contains loops has more no. of atoms as compared to other str. without loop insertion .. so which way it can be analyzed ?? Also g_rmsf gives RMSF values for atoms of residues but not of residues how can I get the values for residues .. Pls help ?? On Tue, Feb 8, 2011 at 6:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Hi, I want to calculate the RMSF of residues and not of protein ... how can this be done with g_rmsf.. Also I want to see the rmsf of certain residues .. for which I created the .ndx file containint those residues only .. and after using g_rmsf with index file gives the RMSF for whole protein backbone and not for that index file residues ... what shall I do to have RMSF of index file residues ?? The default output of g_rmsf is a plot of RMSF (of each residue) vs. residue. No index file is required to obtain this, unless you want to do the fitting to some custom group. Is this not what you want? -Justin -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_rmsf
bharat gupta wrote: Actually after loop incorporation I want to check which region of the protein shows much deviation , which I think can be done by plotting rmsf values from both proteins.. but the problem here is that one structure which contains loops has more no. of atoms as compared to other str. without loop insertion .. so which way it can be analyzed ?? Also g_rmsf gives RMSF values for atoms of residues but not of residues how can I get the values for residues .. Please read g_rmsf -h. -Justin Pls help ?? On Tue, Feb 8, 2011 at 6:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bharat gupta wrote: Hi, I want to calculate the RMSF of residues and not of protein ... how can this be done with g_rmsf.. Also I want to see the rmsf of certain residues .. for which I created the .ndx file containint those residues only .. and after using g_rmsf with index file gives the RMSF for whole protein backbone and not for that index file residues ... what shall I do to have RMSF of index file residues ?? The default output of g_rmsf is a plot of RMSF (of each residue) vs. residue. No index file is required to obtain this, unless you want to do the fitting to some custom group. Is this not what you want? -Justin -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_rmsf
try -res option On Wed, Feb 9, 2011 at 08:51, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Actually after loop incorporation I want to check which region of the protein shows much deviation , which I think can be done by plotting rmsf values from both proteins.. but the problem here is that one structure which contains loops has more no. of atoms as compared to other str. without loop insertion .. so which way it can be analyzed ?? Also g_rmsf gives RMSF values for atoms of residues but not of residues how can I get the values for residues .. Please read g_rmsf -h. -Justin Pls help ?? On Tue, Feb 8, 2011 at 6:57 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: bharat gupta wrote: Hi, I want to calculate the RMSF of residues and not of protein ... how can this be done with g_rmsf.. Also I want to see the rmsf of certain residues .. for which I created the .ndx file containint those residues only .. and after using g_rmsf with index file gives the RMSF for whole protein backbone and not for that index file residues ... what shall I do to have RMSF of index file residues ?? The default output of g_rmsf is a plot of RMSF (of each residue) vs. residue. No index file is required to obtain this, unless you want to do the fitting to some custom group. Is this not what you want? -Justin -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] solvation_box_preparation
Hi Justin Thanks a lot. I tried doing energy minimization and th lowering emtotal to 200 and the system converged to Steepest Descents converged to Fmax 200 in 1411 steps Potential Energy = -3.9063050e+05 Maximum force = 1.3442458e+02 on atom 927 Norm of force = 1.4758101e+01 For equilibration of solvation box I am following a biophys j paper in which protocol for urea box preparation is given. A simulated annealing under high pressure (ref_p=100) to cool system from 300 to 0K thereafter heating back to 300K at ref_p=1. Again 1ns MD at same condition. If this way is harsh treatment of system then suggest me the way out. My sa.mdp sa_hot.mdp and sa_equilibriation.mdp as well as chaps.itp are attached with this mail Shahid Nayeem On Mon, Jan 31, 2011 at 9:47 AM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Please tell me where I am wrong. I downloaded pdb of chaps and used prodrg server to get .itp and .gro file. Then I checked .itp for any missing charge and I found it correct. Then I created 6.0x6.0x6.0 box PRODRG doesn't have a problem of missing charges. It provides notoriously incorrect charges. with genbox inserting 7 molecules of chaps.gro. Then again using genbox and -maxsol I put 510 spc.itp in the box to get a density approaching 1. Then I did steepest descent energy minimization with constraints = none, for emtotal=2000 and emstep=3000. Up to this the These settings make no sense. An emtol of 2000 is very high, and emstep of 3000 is total nonsense. How well did you EM converge? What were the values of the potential energy and maximum force? gromacs runs fine. when I start simulated annealing for cooling at high pressure with constraint = all_bonds the programme gives fatal error linc warning and stops. If I do energy minimization with constraint =all_bonds then also with some error of linc wrning the minimization is completed. When I do minimization without adding water then there is no linc warning and minimization is completed but with final positive potential energy. Then as suggested by Justin I used smaller box and there also in simulated annealing stage the system gives linc warning and the programme stops with fatal error. Please tell me where I am wrong. How about simplifying the problem. Does the system run under normal conditions? In other words, can you run normal MD? You're treating the system very harshly with the combination of high pressure and annealing. Without seeing your .mdp file for this process, it's impossible to say how reasonable your settings are. It is also possible that your parameters for CHAPS (if they are the default ones from PRODRG) are incorrect. The charges and charge groups nearly always are. Without seeing them, there's nothing better to offer. -Justin shahid nayeem On Fri, Jan 28, 2011 at 10:59 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 28/01/2011 3:51 PM, shahid nayeem wrote: Thanks Justin I tried with new box size of 2.8x2.8x2.8 . During energy minimization with steepest descent to force of 2000 and constraint=none, the system converged in 754 steps with positive potential energy. In subsequent simulated annealing with constraint all bonds it starts giving link warning in 0 step with rms 7407.805164, max 66989.116545 (between atom 94 and 117) and a list of bond thar rotated more than 30 degree almost atom number belonging to chaps molecule. You've set up a system that isn't stable, but we don't have enough information to have any idea why. I tried with new box size doesn't go close to describing your method in enough detail for anyone to know where you went wrong. See http://www.gromacs.org/Documentation/Terminology/Blowing_Up for generic tips Mark Please help. shahid Nayeem On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkuljalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am sending this mail again on user list because my reply to Mark’s query was not uploaded on the list. Original messge: I am trying to prepare a solvation box of chaps. After generating .itp and .gro at ProDrg and thorough check of charges, I started with a box size of 6x6x6. Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I get a box where all water molecules get accumulated in two three small region within the box and all chaps molecules gets accumulated in another small regions.I wanted near random uniform distribution of chaps in water. Any help from user, where I am wrong and what should I do. Reply to query. I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox –ci 7 chaps.gro).Then I solvated the output box with genbox using -maxsol 500 and spc216.gro. On visualization, at this stage itself uniform solvation did not occur (I got water in one region and chaps molecule in other region) but I observed a
Re: [gmx-users] Re: g_rmsf
I used the -res option ... and I got the rmsf in terms of residues but still the problem is that the two structures contain different amount of residues due to loop replacement in one structure.. In that case how shall proceed to check the effect of loop insertion on the overall topology of the protein.. pls guide ?? On Tue, Feb 8, 2011 at 7:21 PM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Actually after loop incorporation I want to check which region of the protein shows much deviation , which I think can be done by plotting rmsf values from both proteins.. but the problem here is that one structure which contains loops has more no. of atoms as compared to other str. without loop insertion .. so which way it can be analyzed ?? Also g_rmsf gives RMSF values for atoms of residues but not of residues how can I get the values for residues .. Please read g_rmsf -h. -Justin Pls help ?? On Tue, Feb 8, 2011 at 6:57 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: bharat gupta wrote: Hi, I want to calculate the RMSF of residues and not of protein ... how can this be done with g_rmsf.. Also I want to see the rmsf of certain residues .. for which I created the .ndx file containint those residues only .. and after using g_rmsf with index file gives the RMSF for whole protein backbone and not for that index file residues ... what shall I do to have RMSF of index file residues ?? The default output of g_rmsf is a plot of RMSF (of each residue) vs. residue. No index file is required to obtain this, unless you want to do the fitting to some custom group. Is this not what you want? -Justin -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_rmsf
Hi Bharat, You can do it with post-processing the data you obtain from g_rmfs, if it's okay that the fit uses all residues in either case. Otherwise, you can make an two index files, including only the residues that are common to both. Hope it helps, Tsjerk On Wed, Feb 9, 2011 at 5:58 AM, bharat gupta bharat.85.m...@gmail.com wrote: I used the -res option ... and I got the rmsf in terms of residues but still the problem is that the two structures contain different amount of residues due to loop replacement in one structure.. In that case how shall proceed to check the effect of loop insertion on the overall topology of the protein.. pls guide ?? On Tue, Feb 8, 2011 at 7:21 PM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Actually after loop incorporation I want to check which region of the protein shows much deviation , which I think can be done by plotting rmsf values from both proteins.. but the problem here is that one structure which contains loops has more no. of atoms as compared to other str. without loop insertion .. so which way it can be analyzed ?? Also g_rmsf gives RMSF values for atoms of residues but not of residues how can I get the values for residues .. Please read g_rmsf -h. -Justin Pls help ?? On Tue, Feb 8, 2011 at 6:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bharat gupta wrote: Hi, I want to calculate the RMSF of residues and not of protein ... how can this be done with g_rmsf.. Also I want to see the rmsf of certain residues .. for which I created the .ndx file containint those residues only .. and after using g_rmsf with index file gives the RMSF for whole protein backbone and not for that index file residues ... what shall I do to have RMSF of index file residues ?? The default output of g_rmsf is a plot of RMSF (of each residue) vs. residue. No index file is required to obtain this, unless you want to do the fitting to some custom group. Is this not what you want? -Justin -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com -- 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 list gmx-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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] Re: g_rmsf
You calculate rmsf of both proteins separately and then plot them together and look the region of your interest.. On Wed, Feb 9, 2011 at 10:28, bharat gupta bharat.85.m...@gmail.com wrote: I used the -res option ... and I got the rmsf in terms of residues but still the problem is that the two structures contain different amount of residues due to loop replacement in one structure.. In that case how shall proceed to check the effect of loop insertion on the overall topology of the protein.. pls guide ?? On Tue, Feb 8, 2011 at 7:21 PM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Actually after loop incorporation I want to check which region of the protein shows much deviation , which I think can be done by plotting rmsf values from both proteins.. but the problem here is that one structure which contains loops has more no. of atoms as compared to other str. without loop insertion .. so which way it can be analyzed ?? Also g_rmsf gives RMSF values for atoms of residues but not of residues how can I get the values for residues .. Please read g_rmsf -h. -Justin Pls help ?? On Tue, Feb 8, 2011 at 6:57 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: bharat gupta wrote: Hi, I want to calculate the RMSF of residues and not of protein ... how can this be done with g_rmsf.. Also I want to see the rmsf of certain residues .. for which I created the .ndx file containint those residues only .. and after using g_rmsf with index file gives the RMSF for whole protein backbone and not for that index file residues ... what shall I do to have RMSF of index file residues ?? The default output of g_rmsf is a plot of RMSF (of each residue) vs. residue. No index file is required to obtain this, unless you want to do the fitting to some custom group. Is this not what you want? -Justin -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] Re: g_rmsf
Thanks for the advice and while creating the index file for first 100 common residues it found that both structures shows different no.of atoms. .. how is that possible ?? On Tue, Feb 8, 2011 at 9:00 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bharat, You can do it with post-processing the data you obtain from g_rmfs, if it's okay that the fit uses all residues in either case. Otherwise, you can make an two index files, including only the residues that are common to both. Hope it helps, Tsjerk On Wed, Feb 9, 2011 at 5:58 AM, bharat gupta bharat.85.m...@gmail.com wrote: I used the -res option ... and I got the rmsf in terms of residues but still the problem is that the two structures contain different amount of residues due to loop replacement in one structure.. In that case how shall proceed to check the effect of loop insertion on the overall topology of the protein.. pls guide ?? On Tue, Feb 8, 2011 at 7:21 PM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Actually after loop incorporation I want to check which region of the protein shows much deviation , which I think can be done by plotting rmsf values from both proteins.. but the problem here is that one structure which contains loops has more no. of atoms as compared to other str. without loop insertion .. so which way it can be analyzed ?? Also g_rmsf gives RMSF values for atoms of residues but not of residues how can I get the values for residues .. Please read g_rmsf -h. -Justin Pls help ?? On Tue, Feb 8, 2011 at 6:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bharat gupta wrote: Hi, I want to calculate the RMSF of residues and not of protein ... how can this be done with g_rmsf.. Also I want to see the rmsf of certain residues .. for which I created the .ndx file containint those residues only .. and after using g_rmsf with index file gives the RMSF for whole protein backbone and not for that index file residues ... what shall I do to have RMSF of index file residues ?? The default output of g_rmsf is a plot of RMSF (of each residue) vs. residue. No index file is required to obtain this, unless you want to do the fitting to some custom group. Is this not what you want? -Justin -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering
Re: [gmx-users] Re: g_rmsf
We can't know that. We don't have your files (and we don't want them). Check what you did, and what index groups you have. Write out the structure for the index group and have a look. We're not a substitute for your brain here... :p Cheers, Tsjerk On Wed, Feb 9, 2011 at 6:20 AM, bharat gupta bharat.85.m...@gmail.com wrote: Thanks for the advice and while creating the index file for first 100 common residues it found that both structures shows different no.of atoms. .. how is that possible ?? On Tue, Feb 8, 2011 at 9:00 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bharat, You can do it with post-processing the data you obtain from g_rmfs, if it's okay that the fit uses all residues in either case. Otherwise, you can make an two index files, including only the residues that are common to both. Hope it helps, Tsjerk On Wed, Feb 9, 2011 at 5:58 AM, bharat gupta bharat.85.m...@gmail.com wrote: I used the -res option ... and I got the rmsf in terms of residues but still the problem is that the two structures contain different amount of residues due to loop replacement in one structure.. In that case how shall proceed to check the effect of loop insertion on the overall topology of the protein.. pls guide ?? On Tue, Feb 8, 2011 at 7:21 PM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Actually after loop incorporation I want to check which region of the protein shows much deviation , which I think can be done by plotting rmsf values from both proteins.. but the problem here is that one structure which contains loops has more no. of atoms as compared to other str. without loop insertion .. so which way it can be analyzed ?? Also g_rmsf gives RMSF values for atoms of residues but not of residues how can I get the values for residues .. Please read g_rmsf -h. -Justin Pls help ?? On Tue, Feb 8, 2011 at 6:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bharat gupta wrote: Hi, I want to calculate the RMSF of residues and not of protein ... how can this be done with g_rmsf.. Also I want to see the rmsf of certain residues .. for which I created the .ndx file containint those residues only .. and after using g_rmsf with index file gives the RMSF for whole protein backbone and not for that index file residues ... what shall I do to have RMSF of index file residues ?? The default output of g_rmsf is a plot of RMSF (of each residue) vs. residue. No index file is required to obtain this, unless you want to do the fitting to some custom group. Is this not what you want? -Justin -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com -- 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 list gmx-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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] Re: No residue type for 'ARG' as a starting terminus
On 8/02/2011 9:27 PM, bipin singh wrote: Hi all, I am getting following during while running pdb2gmx for a RNA moleculei am using amber99sb force field parameters The details of the error is as: Fatal error: In the chosen force field there is no residue type for 'ARG' as a starting terminus For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Sounds like you have an arginine residue. Why? 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] OPLS and RB parameters in GROMACS
I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121, 20, 4831, 1999), the aliphatic torsional parameters are the same as those from 1996. here are the values, V1 V2V3 (kcal/mol) CT-CT-CT-CT 1.740 -0.157 0.279 HC-CT-CT-CT 0.0000.0000.366 HC-CT-CT-HC 0.000 0.000 0.318 Values calculated from the equation given in p.62 of the manual in kJ/mol are c0 c1 c2 c3 CT-CT-CT-CT 3.56686-1.88907 0.65688-2.33467 HC-CT-CT-CT 0.66526 1.99577 0.000 -2.66102 HC-CT-CT-HC 0.76567-2.29702 0.000 -3.06269 and the values given in ffoplsaabon.itp are: CT-CT-CT-CT 2.9288-1.46440.2092 -1.6736 HC-CT-CT-CT 0.6276 1.88280 0.000 -2.5104 HC-CT-CT-HC 0.62761.8828 0.000 -2.5104 So there is a difference. Which of these is correct ? Any help is highly appreciated. Sulatha On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch apal...@nd.edu wrote: There is no error. The alkane dihedral parameters were updated in 1999, and differ from those originally published in 1996. Andrew On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S mssula...@gmail.com wrote: Hi all, Hi I've converted the OPLS-AA torsional potential parameters for the alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation), C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found that the calculated values are different. A previous post to the gmx-users mailing list on March 27, 2008, pointed out this issue for the H-C-C-H torsional potential but there was no response to that. Does anyone know if there is an error in the ffoplsaabon.itp file? Or is there a newer set of OPLS-AA parameters? For the OPLS-AA parameters (in kcal/mol), I used: dihedral V1 V2 V3 C-C-C-C1.740 -0.157 0.279 C-C-C-H 0.0 0.00.366 H-C-C-H 0.0 0.00.318 from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as: dihedral C0 C1 C2 C3 C-C-C-C3.56686 -1.889076 0.65688 -2.33467 C-C-C-H 0.66526 1.99577 0.0 -2.661024 H-C-C-H 0.76567 -2.297020.0 -3.06269 the parameters in the ffoplsaabon.itp file are: dihedral C0 C1 C2 C3 C-C-C-C 2.9288 -1.4644 0.2092 -1.6736 C-C-C-H 0.6276 1.882800.0 -2.5104 H-C-C-H 0.6276 1.8828 0.0 -2.5104 Thankyou for any clarification. Sulatha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_rmsf
Tsjerk, Sorry for asking that .. actually I made a silly mistake while selecting residues.. After plotting the graphs for common regions I found that first 100 amino acids shows a lot of fluctuations (compared to the one without any loop insertion) ... Does the insertion caused a great change in the over topology ... what could be the answer for this ?? ... Is there any other way to check the effect loop insertion on the topology of protein ... I heard of essential dynamics method and I asked u earlier about the same .. u told me that 3ns time is small for such analysis but I have found a paper (published in 1999) that has done ED analysis on a 1ns simulated trajectory .. Whether doing such analysis for my data will be acceptable ?? I also want to know how can I calculate the distance between two beta strands (which are connected by a loop) ... On Tue, Feb 8, 2011 at 9:26 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: We can't know that. We don't have your files (and we don't want them). Check what you did, and what index groups you have. Write out the structure for the index group and have a look. We're not a substitute for your brain here... :p Cheers, Tsjerk On Wed, Feb 9, 2011 at 6:20 AM, bharat gupta bharat.85.m...@gmail.com wrote: Thanks for the advice and while creating the index file for first 100 common residues it found that both structures shows different no.of atoms. .. how is that possible ?? On Tue, Feb 8, 2011 at 9:00 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bharat, You can do it with post-processing the data you obtain from g_rmfs, if it's okay that the fit uses all residues in either case. Otherwise, you can make an two index files, including only the residues that are common to both. Hope it helps, Tsjerk On Wed, Feb 9, 2011 at 5:58 AM, bharat gupta bharat.85.m...@gmail.com wrote: I used the -res option ... and I got the rmsf in terms of residues but still the problem is that the two structures contain different amount of residues due to loop replacement in one structure.. In that case how shall proceed to check the effect of loop insertion on the overall topology of the protein.. pls guide ?? On Tue, Feb 8, 2011 at 7:21 PM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Actually after loop incorporation I want to check which region of the protein shows much deviation , which I think can be done by plotting rmsf values from both proteins.. but the problem here is that one structure which contains loops has more no. of atoms as compared to other str. without loop insertion .. so which way it can be analyzed ?? Also g_rmsf gives RMSF values for atoms of residues but not of residues how can I get the values for residues .. Please read g_rmsf -h. -Justin Pls help ?? On Tue, Feb 8, 2011 at 6:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bharat gupta wrote: Hi, I want to calculate the RMSF of residues and not of protein ... how can this be done with g_rmsf.. Also I want to see the rmsf of certain residues .. for which I created the .ndx file containint those residues only .. and after using g_rmsf with index file gives the RMSF for whole protein backbone and not for that index file residues ... what shall I do to have RMSF of index file residues ?? The default output of g_rmsf is a plot of RMSF (of each residue) vs. residue. No index file is required to obtain this, unless you want to do the fitting to some custom group. Is this not what you want? -Justin -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com -- 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/Support/Mailing_Lists/Search before posting! Please don't post
Re: [gmx-users] Re: No residue type for 'ARG' as a starting terminus
Sir, Actually ARG is present as a ligand bound to RNA molecule On Wed, Feb 9, 2011 at 11:16, Mark Abraham mark.abra...@anu.edu.au wrote: On 8/02/2011 9:27 PM, bipin singh wrote: Hi all, I am getting following during while running pdb2gmx for a RNA moleculei am using amber99sb force field parameters The details of the error is as: Fatal error: In the chosen force field there is no residue type for 'ARG' as a starting terminus For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Sounds like you have an arginine residue. Why? 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] OPLS and RB parameters in GROMACS
On 9/02/2011 4:48 PM, sulatha M. S wrote: I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121, 20, 4831, 1999), the aliphatic torsional parameters are the same as those from 1996. here are the values, V1 V2V3 (kcal/mol) CT-CT-CT-CT 1.740 -0.157 0.279 HC-CT-CT-CT 0.0000.0000.366 HC-CT-CT-HC 0.000 0.000 0.318 Values calculated from the equation given in p.62 of the manual in kJ/mol are I can see nothing relevant on p62 of the 4.5 manual. When giving references to literature that exists in multiple versions, please be very precise. Giving details such as the manual version number, page number, equation number and description of the relationship described in the equation will make it much more likely that someone will (want to) (be able to) help you. Mark c0 c1 c2 c3 CT-CT-CT-CT 3.56686-1.88907 0.65688-2.33467 HC-CT-CT-CT 0.66526 1.99577 0.000 -2.66102 HC-CT-CT-HC 0.76567-2.29702 0.000 -3.06269 and the values given in ffoplsaabon.itp are: CT-CT-CT-CT 2.9288-1.4644 0.2092 -1.6736 HC-CT-CT-CT 0.6276 1.88280 0.000 -2.5104 HC-CT-CT-HC 0.62761.8828 0.000 -2.5104 So there is a difference. Which of these is correct ? Any help is highly appreciated. Sulatha On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch apal...@nd.edu mailto:apal...@nd.edu wrote: There is no error. The alkane dihedral parameters were updated in 1999, and differ from those originally published in 1996. Andrew On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S mssula...@gmail.com mailto:mssula...@gmail.com wrote: Hi all, Hi I've converted the OPLS-AA torsional potential parameters for the alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation), C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found that the calculated values are different. A previous post to the gmx-users mailing list on March 27, 2008, pointed out this issue for the H-C-C-H torsional potential but there was no response to that. Does anyone know if there is an error in the ffoplsaabon.itp file? Or is there a newer set of OPLS-AA parameters? For the OPLS-AA parameters (in kcal/mol), I used: dihedral V1 V2 V3 C-C-C-C 1.740 -0.157 0.279 C-C-C-H 0.0 0.0 0.366 H-C-C-H 0.0 0.0 0.318 from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as: dihedral C0C1 C2C3 C-C-C-C 3.56686-1.8890760.65688 -2.33467 C-C-C-H 0.665261.99577 0.0-2.661024 H-C-C-H 0.76567-2.29702 0.0-3.06269 the parameters in the ffoplsaabon.itp file are: dihedral C0 C1 C2C3 C-C-C-C2.9288 -1.4644 0.2092 -1.6736 C-C-C-H0.62761.88280 0.0-2.5104 H-C-C-H0.62761.8828 0.0-2.5104 Thankyou for any clarification. Sulatha -- gmx-users mailing list gmx-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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-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/Support/Mailing_Lists/Search
Re: [gmx-users] Re: g_rmsf
On 9/02/2011 4:52 PM, bharat gupta wrote: Tsjerk, Sorry for asking that .. actually I made a silly mistake while selecting residues.. After plotting the graphs for common regions I found that first 100 amino acids shows a lot of fluctuations (compared to the one without any loop insertion) ... Does the insertion caused a great change in the over topology ... what could be the answer for this ?? ... Maybe the insertion does cause a change. Isn't that one of the things you're trying to see? Maybe you've not got enough data. Maybe you've not made a single-variable change. You have to have done a pair of simulations (whose difference is known, well-defined and relevant) for long enough time for the observables to converge within a simulation in order to do a meaningful comparison of those observables across those simulations. Is there any other way to check the effect loop insertion on the topology of protein ... I heard of essential dynamics method and I asked u earlier about the same .. u told me that 3ns time is small for such analysis but I have found a paper (published in 1999) that has done ED analysis on a 1ns simulated trajectory .. Whether doing such analysis for my data will be acceptable ?? Computer power doubles about every 18 months. Things that were too-short-but-acceptable a decade ago often will no longer be acceptable. In the 80s people did vacuum MD with 0.7nm cutoffs, which would be laughed at now. I also want to know how can I calculate the distance between two beta strands (which are connected by a loop) Have a look at the short descriptions of the the tools in manual section 7.4 or 8, and then look up the detailed descriptions of useful-sounding tools in the appendix. Mark ... On Tue, Feb 8, 2011 at 9:26 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: We can't know that. We don't have your files (and we don't want them). Check what you did, and what index groups you have. Write out the structure for the index group and have a look. We're not a substitute for your brain here... :p Cheers, Tsjerk On Wed, Feb 9, 2011 at 6:20 AM, bharat gupta bharat.85.m...@gmail.com mailto:bharat.85.m...@gmail.com wrote: Thanks for the advice and while creating the index file for first 100 common residues it found that both structures shows different no.of atoms. .. how is that possible ?? On Tue, Feb 8, 2011 at 9:00 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Bharat, You can do it with post-processing the data you obtain from g_rmfs, if it's okay that the fit uses all residues in either case. Otherwise, you can make an two index files, including only the residues that are common to both. Hope it helps, Tsjerk On Wed, Feb 9, 2011 at 5:58 AM, bharat gupta bharat.85.m...@gmail.com mailto:bharat.85.m...@gmail.com wrote: I used the -res option ... and I got the rmsf in terms of residues but still the problem is that the two structures contain different amount of residues due to loop replacement in one structure.. In that case how shall proceed to check the effect of loop insertion on the overall topology of the protein.. pls guide ?? On Tue, Feb 8, 2011 at 7:21 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bharat gupta wrote: Actually after loop incorporation I want to check which region of the protein shows much deviation , which I think can be done by plotting rmsf values from both proteins.. but the problem here is that one structure which contains loops has more no. of atoms as compared to other str. without loop insertion .. so which way it can be analyzed ?? Also g_rmsf gives RMSF values for atoms of residues but not of residues how can I get the values for residues .. Please read g_rmsf -h. -Justin Pls help ?? On Tue, Feb 8, 2011 at 6:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: bharat gupta wrote: Hi, I want to calculate the RMSF of residues and not of protein ... how can this be done with g_rmsf.. Also I want to see the rmsf of certain residues .. for which I created the .ndx file containint those residues only .. and after using g_rmsf with index file gives the RMSF for whole protein backbone and not for that index file residues ... what shall I do to have RMSF of index file residues ?? The default output of g_rmsf is a plot of
Re: [gmx-users] Re: No residue type for 'ARG' as a starting terminus
Thanks for your help. On Wed, Feb 9, 2011 at 11:44, Mark Abraham mark.abra...@anu.edu.au wrote: On 9/02/2011 4:56 PM, bipin singh wrote: Sir, Actually ARG is present as a ligand bound to RNA molecule Then you've got work to do. pdb2gmx copes well with linear polymers of predefined monomers, which you don't have. You will need to become very conversant with chapter 5 of the manual. Various how-tos on the wiki will help too. One solution is to generate a topology for base-bound-to-arginine by hand based on the building blocks in the respective .rtp files. Check that topology is useful for vacuum MD of that hybrid residue. Then modify it to be a new .rtp entry, update the forcefield database accordingly. Only then can pdb2gmx deal with it. Another is to use AMBER's leap module to generate a topology for base-bound-to-arginine, and convert the topology representation somehow (IIRC there might be a tool for that). Then proceed as above. Mark On Wed, Feb 9, 2011 at 11:16, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/02/2011 9:27 PM, bipin singh wrote: Hi all, I am getting following during while running pdb2gmx for a RNA moleculei am using amber99sb force field parameters The details of the error is as: Fatal error: In the chosen force field there is no residue type for 'ARG' as a starting terminus For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Sounds like you have an arginine residue. Why? 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] OPLS and RB parameters in GROMACS
Sorry for not giving the manual version earlier. P. 63 of manual 4.0 is what I am referring to. The equations relate to converting the OPLS torsional parameters to RB parameters in GROMACS with the OPLS ff. The equations are C0 = V0+V2+0.5(V1+V3) C1= 0.5(3 * V3-V1) C2= -V2 + 4 * V4 C3= -2 * V3 C4= -4 * V4 Thanks Sulatha On Wed, Feb 9, 2011 at 11:31 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/02/2011 4:48 PM, sulatha M. S wrote: I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121, 20, 4831, 1999), the aliphatic torsional parameters are the same as those from 1996. here are the values, V1 V2V3 (kcal/mol) CT-CT-CT-CT 1.740 -0.157 0.279 HC-CT-CT-CT 0.0000.0000.366 HC-CT-CT-HC 0.000 0.000 0.318 Values calculated from the equation given in p.62 of the manual in kJ/mol are I can see nothing relevant on p62 of the 4.5 manual. When giving references to literature that exists in multiple versions, please be very precise. Giving details such as the manual version number, page number, equation number and description of the relationship described in the equation will make it much more likely that someone will (want to) (be able to) help you. Mark c0 c1 c2 c3 CT-CT-CT-CT 3.56686-1.88907 0.65688-2.33467 HC-CT-CT-CT 0.66526 1.99577 0.000 -2.66102 HC-CT-CT-HC 0.76567-2.29702 0.000 -3.06269 and the values given in ffoplsaabon.itp are: CT-CT-CT-CT 2.9288-1.46440.2092 -1.6736 HC-CT-CT-CT 0.6276 1.88280 0.000 -2.5104 HC-CT-CT-HC 0.62761.8828 0.000 -2.5104 So there is a difference. Which of these is correct ? Any help is highly appreciated. Sulatha On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch apal...@nd.edu wrote: There is no error. The alkane dihedral parameters were updated in 1999, and differ from those originally published in 1996. Andrew On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S mssula...@gmail.comwrote: Hi all, Hi I've converted the OPLS-AA torsional potential parameters for the alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation), C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found that the calculated values are different. A previous post to the gmx-users mailing list on March 27, 2008, pointed out this issue for the H-C-C-H torsional potential but there was no response to that. Does anyone know if there is an error in the ffoplsaabon.itp file? Or is there a newer set of OPLS-AA parameters? For the OPLS-AA parameters (in kcal/mol), I used: dihedral V1 V2 V3 C-C-C-C1.740 -0.157 0.279 C-C-C-H 0.0 0.00.366 H-C-C-H 0.0 0.00.318 from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as: dihedral C0 C1 C2 C3 C-C-C-C3.56686 -1.889076 0.65688 -2.33467 C-C-C-H 0.66526 1.99577 0.0 -2.661024 H-C-C-H 0.76567 -2.297020.0 -3.06269 the parameters in the ffoplsaabon.itp file are: dihedral C0 C1 C2 C3 C-C-C-C 2.9288 -1.4644 0.2092 -1.6736 C-C-C-H 0.6276 1.882800.0 -2.5104 H-C-C-H 0.6276 1.8828 0.0 -2.5104 Thankyou for any clarification. Sulatha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org
[gmx-users] add force field
Hi, Anyone has successfully tried to add some new force field in the default force field (in 4.5) so pdb2gmx can show up the (newly-added) force field which will also be recognized by gromacs, Thanks, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
