[gmx-users] residue IDs are not ordered in gro file.
Hi, there: I found that in gromacs version 4.5.1, the residue ids are not ordered consecutively as before in the .gro file. For example, if I have two chains in the protein, then the residue ids will be ordered with respect to each individual chain, rather than reordered to be a complete system. I also attached one segment in the gro file for illustration. Is this supposed to be a new feature? It's actually quite inconvenient when trying to make selection in VMD. Thanks, Bin == 816VAL HG1313296 3.455 7.611 11.465 0.7230 -0.9675 -4.0812 816VALCG213297 3.630 7.461 11.621 -0.5958 0.7701 0.1938 816VAL HG2113298 3.680 7.555 11.591 0.2600 0.8421 1.7585 816VAL HG2213299 3.571 7.503 11.705 2.5960 0.5799 2.7250 816VAL HG2313300 3.714 7.394 11.646 -0.5850 1.1199 1.1233 816VAL C13301 3.390 7.261 11.629 -0.6898 0.0472 -0.1581 816VALOT113302 3.270 7.268 11.592 -0.7354 -0.1123 -0.0378 816VALOT213303 3.418 7.233 11.749 0.0205 0.1649 -0.2904 8ALA N13304 4.101 8.322 6.962 0.4051 -0.3543 -0.0582 8ALA H113305 4.012 8.374 6.969 1.1832 1.0474 -0.2561 8ALA H213306 4.179 8.374 7.007 -0.8226 0.0271 1.7227 8ALA H313307 4.089 8.236 7.020 -2.0801 -1.0654 -1.4588 8ALA CA13308 4.132 8.290 6.820 0.4700 0.4977 -0.2390 8ALA HA13309 4.051 8.228 6.785 -1.3315 1.9366 1.1423 -- 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] reg error in QM/MM topology
Dear Mark Abraham sir, thank you for your reply i have edited my .top files in gromacs as u said when i run the ./grompp it shows the error as follows ./grompp_d -f em.mdp -c spep_b4em.gro -p spep.top -o spep_em.tpr ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 222 of the 1653 non-bonded parameter combinations --- Program grompp_d, VERSION 4.0.7 Source code file: toppush.c, line: 1379 Fatal error: Incorrect number of parameters - found 2, expected 0 or 0 for Connect Bonds what could i do to avod error? i am expecting your valuable reply -- 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] cubic spline and continuous derivatives
Hi, Yes. Cubic spline interpolation means piecewise interpolation with third order polynomials. The terms says nothing about which derivatives are continuous. Cubic spline interpolation is often used to interpolate between points where only the function value itself is provided and in that case one usually chooses to match the second derivative at the reference points. But that is just one of the many uses of cubic spline interpolation. Berk Date: Sun, 19 Sep 2010 01:32:44 -0700 From: floris_buel...@yahoo.com To: gmx-users@gromacs.org Subject: [gmx-users] cubic spline and continuous derivatives Hello, The gromacs manual states that for cubic spline interpolation of potential energy and forces, V and V’ are continuous, while V” is the first discontinuous derivative. This makes sense to me as there is a unique solution for parameters A2 and A3 if V and V' to the left and right are given for each piecewise polynomial. However the definition of a cubic spline seems to be for a set of functions continous up to the second derivative. Is the cubic spline formulation used somehow unorthodox in this sense? I'm using a similar scheme in a slightly different context, is it strictly correct to refer to it as cubic spline interpolation? Thanks, Floris -- 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] genbox and martini, ethanol solvent
Dear users, I'm trying to create a box with a number (64) of small peptide molecules (diphenylalanine) solved in ethanol for a Gromacs run with the Martini coarse-grain force field. I've created the box with the solute with the genbox -ci command: genbox -ci FFMM_cg.pdb -nmol 64 -box 5 5 5 -o FFMM_box.gro. This all seemed to work fine and I confirmed that it worked in VMD. However, when I try to fill the box with ethanol, this gives problems: genbox -cp FFMM_box.gro -cs ethanol_cg.pdb gets stuck at Reading solvent configuration solvent configuration contains 1 atoms in 1 residues (no error message, but just stops). 1 atom in 1 residue is correct for my pdb file, since ethanol is represented by 1 atom in Martini. I have tried to circumvent this problem by using the ci option again to add ethanol molecules 1 by 1. This kind of works, but if I try it for too many molecules (nmol 15000) it crashes as well with the message 'killed'. Also solving in ethanol that's not converted to coarse grain gets stuck (except from that it says 9 atoms in 1 residue). I have tried to solve it in the spc216 water, this works, so there must be something wrong with my pdb file for the solvent. I can see in other solvent gro/pdb files that there are usually a lot of solvent molecules in 1 file. Why is that and what can I do to make the ethanol box? Thanks very much in advance, Pim PhD student University of Strathclyde Pure Applied Chemistry / Biomolecular and Chemical Physics -- 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] Energy Minimzation with Gromacs leads to distortion of planar groups
NG HUI WEN wrote: Dear Gmxusers, I have noticed that energy minimization with gromacs (gromos G53a6 forcefield) had led to the distortion of sidechain planarity in my protein model. Comparison of PROCEHCK results between the pre- and post energy minimized structures have shown an increase in the number of distorted planar groups (e.g. rings and non-ring aliphatic groups). As steepest descent seem to converge very rapidly (500 steps) to machine precision, I also tried using the conjugate gradient and lbfgs methods. What were the values of the potential and maximum force when EM converged? -Justin The .mdp files used are as follow. Steepest descent title = Energy Minimization without position restraint cpp = /lib/cpp ; Preprocessor define= -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps= 500 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple; Method to determine neighbor list (simple, grid) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off constraints = none; Bond types to replace by constraints pbc = no; Periodic Boundary Conditions (yes/no) CG title = Energy Minimization with out position restraint cpp = /lib/cpp ; Preprocessor define= -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = cg; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol dt = 0.0001 nsteps= 500 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple; Method to determine neighbor list (simple, grid) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off constraints = none; Bond types to replace by constraints pbc = no; Periodic Boundary Conditions (yes/no) lbfgs title = Energy Minimization without position restraint cpp = /lib/cpp ; Preprocessor define= -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = l-bfgs ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps= 1500; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple; Method to determine neighbor list (simple, grid) coulombtype = pme ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; long range electrostatic cut-off vdwtype = switch rlist = 1.2 rvdw= 1.0 ; long range Van der Waals cut-off rvdw-switch = 0.8 constraints = none; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) I might have done something wrongly to cause this. Would really appreciate it if someone could enlighten me on this. Thanks!! HW Email has been scanned for viruses by UNMC email management service http://www.nottingham.edu.my -- 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
RE: [gmx-users] Energy Minimzation with Gromacs leads to distortion of planar groups
Try without -DFLEXIBLE. See this message: http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html Andreas --- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of NG HUI WEN Sent: 20 September 2010 04:21 To: gmx-users@gromacs.org Subject: [gmx-users] Energy Minimzation with Gromacs leads to distortion of planar groups Dear Gmxusers, I have noticed that energy minimization with gromacs (gromos G53a6 forcefield) had led to the distortion of sidechain planarity in my protein model. Comparison of PROCEHCK results between the pre- and post energy minimized structures have shown an increase in the number of distorted planar groups (e.g. rings and non-ring aliphatic groups). As steepest descent seem to converge very rapidly (500 steps) to machine precision, I also tried using the conjugate gradient and lbfgs methods. The .mdp files used are as follow. Steepest descent title = Energy Minimization without position restraint cpp = /lib/cpp ; Preprocessor define= -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps= 500 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple; Method to determine neighbor list (simple, grid) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off constraints = none; Bond types to replace by constraints pbc = no; Periodic Boundary Conditions (yes/no) CG title = Energy Minimization with out position restraint cpp = /lib/cpp ; Preprocessor define= -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = cg; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol dt = 0.0001 nsteps= 500 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple; Method to determine neighbor list (simple, grid) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off constraints = none; Bond types to replace by constraints pbc = no; Periodic Boundary Conditions (yes/no) lbfgs title = Energy Minimization without position restraint cpp = /lib/cpp ; Preprocessor define= -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = l-bfgs ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps= 1500; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple; Method to determine neighbor list (simple, grid) coulombtype = pme ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; long range electrostatic cut-off vdwtype = switch rlist = 1.2 rvdw= 1.0 ; long range Van der Waals cut-off rvdw-switch = 0.8 constraints = none; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) I might have done something wrongly to cause this. Would really appreciate it if someone could enlighten me on this. Thanks!! HW Email has been scanned for viruses by UNMC email management service -- 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] Energy Minimzation with Gromacs leads to distortion of planar groups
Kukol, Andreas wrote: Try without -DFLEXIBLE. See this message: http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html Doesn't -DFLEXIBLE only affect water, not the aromatic rings of the protein? Don't the real problems come from running actual MD with -DFLEXBILE? In some cases for EM, it has even been recommended. -Justin Andreas --- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of NG HUI WEN Sent: 20 September 2010 04:21 To: gmx-users@gromacs.org Subject: [gmx-users] Energy Minimzation with Gromacs leads to distortion of planar groups Dear Gmxusers, I have noticed that energy minimization with gromacs (gromos G53a6 forcefield) had led to the distortion of sidechain planarity in my protein model. Comparison of PROCEHCK results between the pre- and post energy minimized structures have shown an increase in the number of distorted planar groups (e.g. rings and non-ring aliphatic groups). As steepest descent seem to converge very rapidly (500 steps) to machine precision, I also tried using the conjugate gradient and lbfgs methods. The .mdp files used are as follow. Steepest descent title = Energy Minimization without position restraint cpp = /lib/cpp ; Preprocessor define= -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps= 500 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple; Method to determine neighbor list (simple, grid) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off constraints = none; Bond types to replace by constraints pbc = no; Periodic Boundary Conditions (yes/no) CG title = Energy Minimization with out position restraint cpp = /lib/cpp ; Preprocessor define= -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = cg; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol dt = 0.0001 nsteps= 500 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple; Method to determine neighbor list (simple, grid) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off constraints = none; Bond types to replace by constraints pbc = no; Periodic Boundary Conditions (yes/no) lbfgs title = Energy Minimization without position restraint cpp = /lib/cpp ; Preprocessor define= -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = l-bfgs ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps= 1500; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple; Method to determine neighbor list (simple, grid) coulombtype = pme ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; long range electrostatic cut-off vdwtype = switch rlist = 1.2 rvdw= 1.0 ; long range Van der Waals cut-off rvdw-switch = 0.8 constraints = none; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) I might have done something wrongly to cause this. Would really appreciate it if someone could enlighten me on this. Thanks!! HW Email has been scanned for viruses by UNMC email management service -- 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
Re: [gmx-users] genbox and martini, ethanol solvent
Pim Frederix wrote: Dear users, I'm trying to create a box with a number (64) of small peptide molecules (diphenylalanine) solved in ethanol for a Gromacs run with the Martini coarse-grain force field. I've created the box with the solute with the genbox -ci command: genbox -ci FFMM_cg.pdb -nmol 64 -box 5 5 5 -o FFMM_box.gro. This all seemed to work fine and I confirmed that it worked in VMD. However, when I try to fill the box with ethanol, this gives problems: genbox -cp FFMM_box.gro -cs ethanol_cg.pdb gets stuck at Reading solvent configuration solvent configuration contains 1 atoms in 1 residues (no error message, but just stops). 1 atom in 1 residue is correct for my pdb file, since ethanol is represented by 1 atom in Martini. I have tried to circumvent this problem by using the ci option again to add ethanol molecules 1 by 1. This kind of works, but if I try it for too many molecules (nmol 15000) it crashes as well with the message 'killed'. Also solving in ethanol that's not converted to coarse grain gets stuck (except from that it says 9 atoms in 1 residue). I have tried to solve it in the spc216 water, this works, so there must be something wrong with my pdb file for the solvent. I can see in other solvent gro/pdb files that there are usually a lot of solvent molecules in 1 file. Why is that and what can I do to make the ethanol box? Using -ci -nmol is prone to running out of memory, which is probably what's happening in your case. If you use genbox -cs, the configuration in the solvent coordinate file is expected to contain multiple atoms, or at the very least, multiple molecules. You can generate a box of CG ethanol using genconf -nbox (to make a grid), then equilibrate. Use this configuration as your solvent using genbox -cs. -Justin Thanks very much in advance, Pim PhD student University of Strathclyde Pure Applied Chemistry / Biomolecular and Chemical Physics -- 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
[gmx-users] Umbrella sampling question
Aswathy: We can't tell if you did US correctly unless you post what you have done. You must give more info and you must copy and paste the actual input / .mdp parameters that you used. As for if your PMF is correct, then we can never tell you that. You can, however, ensure that your sampling distributions are compatible with the PMF that you get out of WHAM by looking at the probability histograms and ensuring that they tend away from the center of restraint and toward local minima on your PMF. There are hundreds of reasons why your PMF might be wrong (note that it also might be correct!) but that is impossible for us to tell with the information that you have provided. At the very least, one would need to see the PMF and all of the info I mentioned above. Also, you should check (and show us!) convergence. If you PMF is still drifting with increasing sampling (or increased initial time discarded as equilibration) then you are simply not converged for sure. Chris. -- original message -- Hi Gromacs users, Let me give an idea about what i am doing. I was doing a Steered Molecular dynamics of ligand transport through the transporter channel. I want to do the PMF calculation using Umbrella sampling. I followed the steps provided in the (Justin's) tutorial. I have generated all configurations, then used the perl script to find out the distance. I made one index group for 3 back bone atoms at the center of the channel and another for the ligand. (Therefore I will get the distance between the center of the channel and ligand). Then I sampled each frame with a window spacing of 0.1nm. The frame close to the center of the channel is taken at the 0 th coordinate(pull_init=0 0 0). above this point is +Z coordinate and below this point is -Z coordinate. I had good overlapped histograms and went ahead with plotting PMF. Am I doing the correct procedure for Umbrella sampling? Why I doubt because, I run g_wham and I had a PMF plot in which at the starting of the transport (from extracellular), I have free energy value of -35kcal/mol. Then as it moves along the pathway it increases and finally it reaches a positive value, +5kcal (when at intracellular). I know its hard give explanation to my observation, but I am confused due to several reasons. 1.The energy increases is not much explainable with interactions of ligand and transporter. 2.If I take the free energy barrier value it is great value than I expected. Nearly 170KJ/mol 3.In similar kind of ligand transport Smds the PMF was continuous maxima and minima. Can any one tell whether my US procedures were right or not? Thanks, -- Aswathy -- 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] Is it possible to use the standard functional forms for the potentials and tabulated ones at the same time?
I have a question regarding potential forms used in GROMACS: Is it possible to use the standard functional forms for the potentials and tabulated ones at the same time? The system I'm looking at is a molecule on a surface. And ideally I want to tabulate the surface interactions and treat the rest of the interactions (nonbonded inter- and intramolecular interactions between two molecules) with simple combination rules. Is that possible? Or is it that once I tabulate one interaction, I have to tabulate the others as well? Thanks. Claudia -- 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] Is it possible to use the standard functional forms for the potentials and tabulated ones at the same time?
Hi, To avoid complex book keeping and parameter checking, you can only run with no tabulated interactions or all tabulated interactions. But there are standard tables for LJ+Coulomb in the share/top directory. I don't know what you mean with surface. A uniform surface can be done with a tabulated potential (see the mdp wall section), that can be combined with standard, non-tabulated non-bonded interactions. Berk From: herb...@csi.tu-darmstadt.de Date: Mon, 20 Sep 2010 15:42:01 +0200 To: gmx-users@gromacs.org Subject: [gmx-users] Is it possible to use the standard functional forms for the potentials and tabulated ones at the same time? I have a question regarding potential forms used in GROMACS: Is it possible to use the standard functional forms for the potentials and tabulated ones at the same time? The system I'm looking at is a molecule on a surface. And ideally I want to tabulate the surface interactions and treat the rest of the interactions (nonbonded inter- and intramolecular interactions between two molecules) with simple combination rules. Is that possible? Or is it that once I tabulate one interaction, I have to tabulate the others as well? Thanks. Claudia -- 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] error on compilation on BlueGene/P
Hi all, I'm trying to install Gromacs on BG/P following the instruction reported here: http://www.gromacs.org/Downloads/Installation_Instructions/GROMACS_on_BlueGene I ran configure: ../configure --prefix=/bgp/userinternal/cin0644a/gromacs \ --enable-ppc-sqrt \ --disable-ppc-altivec \ --enable-fortran \ --with-fft=fftw3 \ --without-x \ CFLAGS=-O3 -qarch=auto -qtune=auto \ CC=xlc_r -q64 \ CXX=xlC_r -q64 \ CXXFLAGS=-O3 -qarch=auto -qtune=auto \ CPPFLAGS=-I/bgp/userinternal/cin0644a/fftwlibs/include \ F77=xlf_r -q64 \ FFLAGS=-O3 -qnoprefetch -qarch=auto -qtune=auto \ LDFLAGS=-L/bgp/userinternal/cin0644a/fftwlibs/lib But when I compile with make I get this error: ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 42.10: 1506-296 (S) #include file nbkernel010_f77_single.h not found. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 43.10: 1506-296 (S) #include file nbkernel020_f77_single.h not found. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 44.10: 1506-296 (S) #include file nbkernel030_f77_single.h not found. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 45.10: 1506-296 (S) #include file nbkernel100_f77_single.h not found. [...] ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 114.5: 1506-045 (S) Undeclared identifier nbkernel010_f77_single. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 115.5: 1506-045 (S) Undeclared identifier nbkernel020_f77_single. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 116.5: 1506-045 (S) Undeclared identifier nbkernel030_f77_single. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 117.5: 1506-045 (S) Undeclared identifier nbkernel100_f77_single. Do you have any hint about that? Thanks in advance! F. -- * Fabio Affinito, PhD CINECA InterUniversity Computer Center Via Magnanelli, 6/3 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) e-mail: f.affin...@cineca.it -- 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] error on compilation on BlueGene/P
... and if I add the --enable-bluegene flag : ../../../../../src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_gen_bluegene.h, line 163.21: 1506-1231 (S) The built-in function __fpsub is not valid for the target architecture. and more similar errors. F. On 09/20/2010 05:35 PM, Fabio Affinito wrote: Hi all, I'm trying to install Gromacs on BG/P following the instruction reported here: http://www.gromacs.org/Downloads/Installation_Instructions/GROMACS_on_BlueGene I ran configure: ../configure --prefix=/bgp/userinternal/cin0644a/gromacs \ --enable-ppc-sqrt \ --disable-ppc-altivec \ --enable-fortran \ --with-fft=fftw3 \ --without-x \ CFLAGS=-O3 -qarch=auto -qtune=auto \ CC=xlc_r -q64 \ CXX=xlC_r -q64 \ CXXFLAGS=-O3 -qarch=auto -qtune=auto \ CPPFLAGS=-I/bgp/userinternal/cin0644a/fftwlibs/include \ F77=xlf_r -q64 \ FFLAGS=-O3 -qnoprefetch -qarch=auto -qtune=auto \ LDFLAGS=-L/bgp/userinternal/cin0644a/fftwlibs/lib But when I compile with make I get this error: ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 42.10: 1506-296 (S) #include file nbkernel010_f77_single.h not found. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 43.10: 1506-296 (S) #include file nbkernel020_f77_single.h not found. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 44.10: 1506-296 (S) #include file nbkernel030_f77_single.h not found. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 45.10: 1506-296 (S) #include file nbkernel100_f77_single.h not found. [...] ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 114.5: 1506-045 (S) Undeclared identifier nbkernel010_f77_single. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 115.5: 1506-045 (S) Undeclared identifier nbkernel020_f77_single. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 116.5: 1506-045 (S) Undeclared identifier nbkernel030_f77_single. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 117.5: 1506-045 (S) Undeclared identifier nbkernel100_f77_single. Do you have any hint about that? Thanks in advance! F. -- * Fabio Affinito, PhD CINECA InterUniversity Computer Center Via Magnanelli, 6/3 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) e-mail: f.affin...@cineca.it -- 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] error on compilation on BlueGene/P
Hi, I think you shouldn't enable fortran. Berk From: f.affin...@cineca.it To: gmx-users@gromacs.org Subject: Re: [gmx-users] error on compilation on BlueGene/P Date: Mon, 20 Sep 2010 17:50:48 +0200 ... and if I add the --enable-bluegene flag : ../../../../../src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_gen_bluegene.h, line 163.21: 1506-1231 (S) The built-in function __fpsub is not valid for the target architecture. and more similar errors. F. On 09/20/2010 05:35 PM, Fabio Affinito wrote: Hi all, I'm trying to install Gromacs on BG/P following the instruction reported here: http://www.gromacs.org/Downloads/Installation_Instructions/GROMACS_on_BlueGene I ran configure: ../configure --prefix=/bgp/userinternal/cin0644a/gromacs \ --enable-ppc-sqrt \ --disable-ppc-altivec \ --enable-fortran \ --with-fft=fftw3 \ --without-x \ CFLAGS=-O3 -qarch=auto -qtune=auto \ CC=xlc_r -q64 \ CXX=xlC_r -q64 \ CXXFLAGS=-O3 -qarch=auto -qtune=auto \ CPPFLAGS=-I/bgp/userinternal/cin0644a/fftwlibs/include \ F77=xlf_r -q64 \ FFLAGS=-O3 -qnoprefetch -qarch=auto -qtune=auto \ LDFLAGS=-L/bgp/userinternal/cin0644a/fftwlibs/lib But when I compile with make I get this error: ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 42.10: 1506-296 (S) #include file nbkernel010_f77_single.h not found. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 43.10: 1506-296 (S) #include file nbkernel020_f77_single.h not found. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 44.10: 1506-296 (S) #include file nbkernel030_f77_single.h not found. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 45.10: 1506-296 (S) #include file nbkernel100_f77_single.h not found. [...] ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 114.5: 1506-045 (S) Undeclared identifier nbkernel010_f77_single. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 115.5: 1506-045 (S) Undeclared identifier nbkernel020_f77_single. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 116.5: 1506-045 (S) Undeclared identifier nbkernel030_f77_single. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 117.5: 1506-045 (S) Undeclared identifier nbkernel100_f77_single. Do you have any hint about that? Thanks in advance! F. -- * Fabio Affinito, PhD CINECA InterUniversity Computer Center Via Magnanelli, 6/3 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) e-mail: f.affin...@cineca.it -- 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] Adding Ions
Hi, I have tried to add NaCl into my system in the 4.5.1 version to balance the total charge, and used OPLS forcefield. In the topol file file, it has CL- but no NA+. However, when I ran grompp_d, it gave me the following error message: Program grompp_d, VERSION 4.5.1 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype CL- It did not happen when I used 4.0.7 version. I checked the top.itp file and CL- is defined. Any clue on how to fix it? Best, Simon -- 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] Adding Ions
simon sham wrote: Hi, I have tried to add NaCl into my system in the 4.5.1 version to balance the total charge, and used OPLS forcefield. In the topol file file, it has CL- but no NA+. However, when I ran grompp_d, it gave me the following error message: Program grompp_d, VERSION 4.5.1 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype CL- It did not happen when I used 4.0.7 version. I checked the top.itp file and CL- is defined. Any clue on how to fix it? Not without seeing the commands you gave that produced this error. Please copy and paste directly from your terminal. -Justin Best, Simon -- 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
[gmx-users] Urea-water
Hello, I am simulating 2M urea in water with single methane (77 urea + 1926 water). I used genbox -ci -nmol to add the number of urea molecules and then used genbox to add water molecules (as suggested in the manual). When I tried to do energy minimization this is what I got : Steepest Descents converged to Fmax 1000 in 234 steps Potential Energy = -1.0054066e+05 So I tried g_energy to plot the potential. But I got average Potential as a positive number 2.84087e+06. I am not sure why the potential is positive, it probably is because of repulsion but is that correct? I would appreciate some help. Thanks. -Nisha P -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Urea-water
On 2010-09-20 19.58, nishap.pa...@utoronto.ca wrote: Hello, I am simulating 2M urea in water with single methane (77 urea + 1926 water). I used genbox -ci -nmol to add the number of urea molecules and then used genbox to add water molecules (as suggested in the manual). When I tried to do energy minimization this is what I got : Steepest Descents converged to Fmax 1000 in 234 steps Potential Energy = -1.0054066e+05 So I tried g_energy to plot the potential. But I got average Potential as a positive number 2.84087e+06. I am not sure why the potential is positive, it probably is because of repulsion but is that correct? Did you look at the graph? Please do, then you will understand. I would appreciate some help. Thanks. -Nisha P -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@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
Re: [gmx-users] Urea-water
I did look at the plot, and it shows that the curve is smoothing right under zero at -1.00e+05 but then why does the average potential show a positive number? Shouldn't that number be negative as well? Quoting David van der Spoel sp...@xray.bmc.uu.se: On 2010-09-20 19.58, nishap.pa...@utoronto.ca wrote: Hello, I am simulating 2M urea in water with single methane (77 urea + 1926 water). I used genbox -ci -nmol to add the number of urea molecules and then used genbox to add water molecules (as suggested in the manual). When I tried to do energy minimization this is what I got : Steepest Descents converged to Fmax 1000 in 234 steps Potential Energy = -1.0054066e+05 So I tried g_energy to plot the potential. But I got average Potential as a positive number 2.84087e+06. I am not sure why the potential is positive, it probably is because of repulsion but is that correct? Did you look at the graph? Please do, then you will understand. I would appreciate some help. Thanks. -Nisha P -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@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 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: Adding Ions
Hi, I have figured the problem. Can't use NA+/CL- in the latest version, and have to use NA/CL at least in OPLS. Best, Simon -- 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] Getting some interesting errors.
Running several free energy perturbation (FEP) runs to further understand how I should set up my larger production runs and I keep getting errors that I cannot find in the gmx-user email or anywhere specifically online. Error 1: I get this error on three of my four runs.The system is a single rna in a water box. Amber03 and tip3p. Two are cyt an the other two are gua. I get through energy minimization (steep) and I fail on positional restriction sd. I can continue on if I turn -dlb on but I get error 2 below. Some interactions seem to be assigned multiple times... This seemed to occur after a restart of a failed job due to loss of HDD available space. I am trying to reproduce this error. Error 2: This error only comes up if I turn -dlb on in the above step. I get through energy minimisation (steep), positional restraint (sd) and I then fail on step 0 of my production run (sd). Getting Loaded... Reading file monomer_md.tpr, VERSION 4.5.1 (single precision) Starting 2 threads Loaded with Money Making 1D domain decomposition 2 x 1 x 1 Back Off! I just backed up dhdl.xvg to ./#dhdl.xvg.1# starting mdrun Protein in water 625000 steps, 2500.0 ps. step 0/opt/gridengine/default/spool/compute-0-15/job_scripts/1877: line 50: 28413 Segmentation fault /home/tjmustard/bin/Gromacs/gromacs-4.5.1-runfolder/bin/g4.5.1-mdrun -v -s monomer_md.tpr -o monomer_md.trr -c monomer_after_pr.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt -dlb no Both jobs are running on a linux cluster running SGE. I have had several jobs finish on this cluster with no problems. I am also running a slightly modified 4.5.1 version. The topsort.c file in the source code was missing a line of code and I was getting Improper Dihedral in ip_pert errors. I have run several methane hydration FEPs with very similar results. I am hoping this is a small problem that can be fixed easily. Thank you for any assistance, TJ Mustard Email: musta...@onid.orst.edu -- 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] Getting some interesting errors.
Hi, Could you file a bugzilla? And what do you mean with -dlb on? on is not an option, the options are: auto, yes, no Thanks, Berk Date: Mon, 20 Sep 2010 12:22:18 -0700 From: musta...@onid.orst.edu To: gmx-users@gromacs.org Subject: [gmx-users] Getting some interesting errors. Message body Running several free energy perturbation (FEP) runs to further understand how I should set up my larger production runs and I keep getting errors that I cannot find in the gmx-user email or anywhere specifically online. Error 1: I get this error on three of my four runs.The system is a single rna in a water box. Amber03 and tip3p. Two are cyt an the other two are gua. I get through energy minimization (steep) and I fail on positional restriction sd. I can continue on if I turn -dlb on but I get error 2 below. Some interactions seem to be assigned multiple times... This seemed to occur after a restart of a failed job due to loss of HDD available space. I am trying to reproduce this error. Error 2: This error only comes up if I turn -dlb on in the above step. I get through energy minimisation (steep), positional restraint (sd) and I then fail on step 0 of my production run (sd). Getting Loaded... Reading file monomer_md.tpr, VERSION 4.5.1 (single precision) Starting 2 threads Loaded with Money Making 1D domain decomposition 2 x 1 x 1 Back Off! I just backed up dhdl.xvg to ./#dhdl.xvg.1# starting mdrun 'Protein in water' 625000 steps, 2500.0 ps. step 0/opt/gridengine/default/spool/compute-0-15/job_scripts/1877: line 50: 28413 Segmentation fault /home/tjmustard/bin/Gromacs/gromacs-4.5.1-runfolder/bin/g4.5.1-mdrun -v -s monomer_md.tpr -o monomer_md.trr -c monomer_after_pr.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt -dlb no Both jobs are running on a linux cluster running SGE. I have had several jobs finish on this cluster with no problems. I am also running a slightly modified 4.5.1 version. The topsort.c file in the source code was missing a line of code and I was getting Improper Dihedral in ip_pert errors. I have run several methane hydration FEP's with very similar results. I am hoping this is a small problem that can be fixed easily. Thank you for any assistance, TJ Mustard Email: musta...@onid.orst.edu -- 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] Getting some interesting errors.
Yes -dlb no not on and I will file a bugzilla. Thanks again Berg Hess. TJ Mustard On September 20, 2010 at 8:38 PM Berk Hess g...@hotmail.com wrote: Hi, Could you file a bugzilla? And what do you mean with -dlb on? on is not an option, the options are: auto, yes, no Thanks, Berk Date: Mon, 20 Sep 2010 12:22:18 -0700 From: musta...@onid.orst.edu To: gmx-users@gromacs.org Subject: [gmx-users] Getting some interesting errors. Running several free energy perturbation (FEP) runs to further understand how I should set up my larger production runs and I keep getting errors that I cannot find in the gmx-user email or anywhere specifically online. Error 1: I get this error on three of my four runs.The system is a single rna in a water box. Amber03 and tip3p. Two are cyt an the other two are gua. I get through energy minimization (steep) and I fail on positional restriction sd. I can continue on if I turn -dlb on but I get error 2 below. Some interactions seem to be assigned multiple times... This seemed to occur after a restart of a failed job due to loss of HDD available space. I am trying to reproduce this error. Error 2: This error only comes up if I turn -dlb on in the above step. I get through energy minimisation (steep), positional restraint (sd) and I then fail on step 0 of my production run (sd). Getting Loaded... Reading file monomer_md.tpr, VERSION 4.5.1 (single precision) Starting 2 threads Loaded with Money Making 1D domain decomposition 2 x 1 x 1 Back Off! I just backed up dhdl.xvg to ./#dhdl.xvg.1# starting mdrun Protein in water 625000 steps, 2500.0 ps. step 0/opt/gridengine/default/spool/compute-0-15/job_scripts/1877: line 50: 28413 Segmentation fault /home/tjmustard/bin/Gromacs/gromacs-4.5.1-runfolder/bin/g4.5.1-mdrun -v -s monomer_md.tpr -o monomer_md.trr -c monomer_after_pr.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt -dlb no Both jobs are running on a linux cluster running SGE. I have had several jobs finish on this cluster with no problems. I am also running a slightly modified 4.5.1 version. The topsort.c file in the source code was missing a line of code and I was getting Improper Dihedral in ip_pert errors. I have run several methane hydration FEPs with very similar results. I am hoping this is a small problem that can be fixed easily. Thank you for any assistance, TJ Mustard Email: musta...@onid.orst.edu -- 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 dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Cant post? Read http://www.gromacs.org/Support/Mailing_Lists TJ Mustard Email: musta...@onid.orst.edu -- 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] residue IDs are not ordered in gro file.
Dear Justin: Thanks a lot for your reply. I indeed have missing residues in the second chain. However, when I try pdb2gmx -renum, it renumbers the second chain starting from 1, rather than starting from 817(Nres_1st+1). Thanks, Bin = 816VAL HG1313296 -3.347 0.716 6.099 816VALCG213297 -3.088 0.611 6.105 816VAL HG2113298 -3.036 0.707 6.088 816VAL HG2213299 -3.131 0.613 6.208 816VAL HG2313300 -3.013 0.530 6.100 816VAL C13301 -3.375 0.483 6.144 816VALOT113302 -3.466 0.460 6.111 816VALOT213303 -3.326 0.517 6.224 1ALA N13304 -2.528 1.672 1.358 1ALA H113305 -2.582 1.754 1.340 1ALA H213306 -2.430 1.694 1.354 1ALA H313307 -2.550 1.635 1.448 1ALA CA13308 -2.558 1.573 1.259 -- 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] residue IDs are not ordered in gro file.
BIN ZHANG wrote: Dear Justin: Thanks a lot for your reply. I indeed have missing residues in the second chain. However, when I try pdb2gmx -renum, it renumbers the second chain starting from 1, rather than starting from 817(Nres_1st+1). To get consecutive numbering, you may have to merge the chains. You can do this with pdb2gmx -chainsep. -Justin Thanks, Bin = 816VAL HG1313296 -3.347 0.716 6.099 816VALCG213297 -3.088 0.611 6.105 816VAL HG2113298 -3.036 0.707 6.088 816VAL HG2213299 -3.131 0.613 6.208 816VAL HG2313300 -3.013 0.530 6.100 816VAL C13301 -3.375 0.483 6.144 816VALOT113302 -3.466 0.460 6.111 816VALOT213303 -3.326 0.517 6.224 1ALA N13304 -2.528 1.672 1.358 1ALA H113305 -2.582 1.754 1.340 1ALA H213306 -2.430 1.694 1.354 1ALA H313307 -2.550 1.635 1.448 1ALA CA13308 -2.558 1.573 1.259 -- 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
[gmx-users] Problem with pdb2gmx and a new residue
Hi All, I'm trying to build a topology for a chromophore-containing protein using Gromacs 4.5 and OPLS-AA. The chromophore is incorporated into the protein's backbone and the parameters all come from a reputable publication, so I've done the following: 1. Created a new .rtp entry 2. Created an .hdb entry 3. Defined all nonbonded parameters for new atomtypes in the .atp and ffnonbonded.itp file 4. Defined all new bonded parameters in ffbonded.itp The coordinate file was then input into pdb2gmx with an oplsaa.ff directory in the working directory. I received the following error (identical with version 4.5 and the most recent git with release-4-5-patches): pdb2gmx -f struct.pdb ... --- Program pdb2gmx, VERSION 4.5.1-20100920-03d181e Source code file: pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue CRO 331 was not found in rtp entry CRO with 39 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The CRO residue is my chromophore. I'm wondering why pdb2gmx is finding an OXT atom in the following coordinates: ... ATOM 2528 N LEU A 330 -13.640 10.888 -25.907 1.00 0.00 ATOM 2529 CA LEU A 330 -12.513 11.013 -26.852 1.00 0.00 ATOM 2530 C LEU A 330 -11.281 10.183 -26.416 1.00 0.00 ATOM 2531 O LEU A 330 -10.625 9.588 -27.277 1.00 0.00 ATOM 2532 CB LEU A 330 -12.159 12.493 -27.066 1.00 0.00 ATOM 2533 CG LEU A 330 -13.206 13.415 -27.691 1.00 0.00 ATOM 2534 CD1 LEU A 330 -12.913 14.905 -27.393 1.00 0.00 ATOM 2535 CD2 LEU A 330 -13.400 13.160 -29.207 1.00 0.00 ATOM 2536 N CRO A 331 -10.669 9.142 -25.611 1.00 0.00 ATOM 2537 CE CRO A 331 -7.407 12.564 -27.240 1.00 0.00 ATOM 2538 SD CRO A 331 -8.035 12.603 -25.595 1.00 0.00 ATOM 2539 CG1 CRO A 331 -8.731 10.996 -25.519 1.00 0.00 ATOM 2540 CB1 CRO A 331 -9.618 10.846 -24.279 1.00 0.00 ATOM 2541 CA1 CRO A 331 -10.227 9.470 -24.406 1.00 0.00 ATOM 2542 C1 CRO A 331 -10.304 8.516 -23.260 1.00 0.00 ATOM 2543 N2 CRO A 331 -9.873 8.765 -21.981 1.00 0.00 ATOM 2544 OH CRO A 331 -8.594 11.111 -15.969 1.00 0.00 ATOM 2545 CD2 CRO A 331 -9.219 9.756 -19.205 1.00 0.00 ATOM 2546 CE2 CRO A 331 -8.888 10.677 -18.207 1.00 0.00 ATOM 2547 CZ CRO A 331 -8.898 10.286 -16.863 1.00 0.00 ATOM 2548 CE1 CRO A 331 -9.219 8.975 -16.518 1.00 0.00 ATOM 2549 CD1 CRO A 331 -9.549 8.056 -17.509 1.00 0.00 ATOM 2550 CG2 CRO A 331 -9.557 8.447 -18.848 1.00 0.00 ATOM 2551 CB2 CRO A 331 -9.880 7.417 -19.857 1.00 0.00 ATOM 2552 CA2 CRO A 331 -10.149 7.645 -21.293 1.00 0.00 ATOM 2553 C2 CRO A 331 -10.726 6.753 -22.143 1.00 0.00 ATOM 2554 O2 CRO A 331 -11.108 5.574 -21.819 1.00 0.00 ATOM 2555 N3 CRO A 331 -10.810 7.255 -23.355 1.00 0.00 ATOM 2556 CA3 CRO A 331 -11.435 6.545 -24.488 1.00 0.00 ATOM 2557 C CRO A 331 -10.492 6.111 -25.580 1.00 0.00 ATOM 2558 O CRO A 331 -10.993 5.596 -26.570 1.00 0.00 ATOM 2559 N VAL A 332 -9.265 5.813 -25.096 1.00 0.00 ATOM 2560 CA VAL A 332 -8.235 4.899 -25.607 1.00 0.00 ATOM 2561 C VAL A 332 -7.512 4.308 -24.397 1.00 0.00 ATOM 2562 O VAL A 332 -6.351 4.567 -24.155 1.00 0.00 ATOM 2563 CB VAL A 332 -7.312 5.633 -26.627 1.00 0.00 ATOM 2564 CG1 VAL A 332 -8.127 5.980 -27.896 1.00 0.00 ATOM 2565 CG2 VAL A 332 -6.687 6.887 -26.051 1.00 0.00 ... Any ideas on what's going on? I can upload a bugzilla if necessary, I just thought I'd report here first since I'm not sure if I'm doing something wrong with respect to the many new pdb2gmx features. -Justin -- 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] Problem with pdb2gmx and a new residue
- Original Message - From: Justin A. Lemkul jalem...@vt.edu Date: Tuesday, September 21, 2010 6:30 Subject: [gmx-users] Problem with pdb2gmx and a new residue To: Gromacs Users' List gmx-users@gromacs.org Hi All, I'm trying to build a topology for a chromophore-containing protein using Gromacs 4.5 and OPLS-AA. The chromophore is incorporated into the protein's backbone and the parameters all come from a reputable publication, so I've done the following:1. Created a new .rtp entry 2. Created an .hdb entry 3. Defined all nonbonded parameters for new atomtypes in the .atp and ffnonbonded.itp file 4. Defined all new bonded parameters in ffbonded.itp I think you need to define CRO as Protein in residuetypes.dat so that the pdb2gmx mechanism can deduce that it should form a C-terminal peptide link in the absence of an end-of-chain marker. Similarly, I have a modified peptide in what's become my system for generating pdb2gmx bugzilla reports, and with 4.5.1 and git head, if I omit the residuetypes.dat definition I see Identified residue ALA1 as a starting terminus. Warning: Residue KCX193 in chain has different type (Other) from starting residue ALA1 (Protein). Warning: Residue ASP194 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASP195 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue GLU196 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASN197 in chain has different type (Protein) from starting residue ALA1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue THR192 as a ending terminus. snip --- Program pdb2gmx_master, VERSION 4.5.1-20100916-6d51340 Source code file: ../../../src/kernel/pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue VAL 467 was not found in rtp entry VAL with 16 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- This is a bit different, inasmuch as I see the error on the final residue of the first chain, rather then on the modified residue, as you do. However pdb2gmx should cope better with this case - clearly it's confused in the above messages about non-matching types. We should probably file a bugzilla, even if this fixes your symptoms. MarkThe coordinate file was then input into pdb2gmx with an oplsaa.ff directory in the working directory. I received the following error (identical with version 4.5 and the most recent git with release-4-5-patches):pdb2gmx -f struct.pdb ... --- Program pdb2gmx, VERSION 4.5.1-20100920-03d181e Source code file: pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue CRO 331 was not found in rtp entry CRO with 39 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ---The CRO residue is my chromophore. I'm wondering why pdb2gmx is finding an OXT atom in the following coordinates:... ATOM 2528 N LEU A 330 -13.640 10.888 -25.9071.00 0.00 ATOM 2529 CA LEU A 330 -12.513 11.013 -26.8521.00 0.00 ATOM 2530 C LEU A 330 -11.281 10.183 -26.4161.00 0.00 ATOM 2531 O LEU A 330 -10.625 9.588 - 27.277 1.00 0.00 ATOM 2532 CB LEU A 330 -12.159 12.493 -27.0661.00 0.00 ATOM 2533 CG LEU A 330 -13.206 13.415 -27.6911.00 0.00 ATOM 2534 CD1 LEU A 330 -12.913 14.905 -27.3931.00 0.00 ATOM 2535 CD2 LEU A 330 -13.400 13.160 -29.2071.00 0.00 ATOM 2536 N CRO A 331 -10.669 9.142 - 25.611 1.00 0.00 ATOM 2537 CE CRO A 331 -7.407 12.564 - 27.240 1.00 0.00 ATOM 2538 SD CRO A 331 -8.035 12.603 - 25.595 1.00 0.00 ATOM 2539 CG1 CRO A 331 -8.731 10.996 - 25.519 1.00 0.00 ATOM 2540 CB1 CRO A 331 -9.618 10.846 - 24.279 1.00 0.00 ATOM 2541 CA1 CRO A 331 -10.227 9.470 - 24.406 1.00 0.00 ATOM 2542 C1 CRO A 331 -10.304 8.516 - 23.260 1.00 0.00 ATOM 2543 N2 CRO A 331 -9.873 8.765 - 21.981 1.00 0.00 ATOM 2544 OH CRO A 331 -8.594 11.111 - 15.969 1.00 0.00 ATOM 2545 CD2 CRO A 331 -9.219 9.756 - 19.205 1.00 0.00 ATOM 2546 CE2 CRO A 331 -8.888 10.677 - 18.207 1.00 0.00 ATOM 2547 CZ CRO A 331 -8.898 10.286 - 16.863 1.00 0.00 ATOM 2548 CE1 CRO A 331 -9.219 8.975 - 16.518 1.00 0.00 ATOM 2549 CD1 CRO A 331
Re: [gmx-users] Problem with pdb2gmx and a new residue
- Original Message - From: Justin A. Lemkul jalem...@vt.edu Date: Tuesday, September 21, 2010 6:30 Subject: [gmx-users] Problem with pdb2gmx and a new residue To: Gromacs Users' List gmx-users@gromacs.org Hi All, I'm trying to build a topology for a chromophore-containing protein using Gromacs 4.5 and OPLS-AA. The chromophore is incorporated into the protein's backbone and the parameters all come from a reputable publication, so I've done the following: 1. Created a new .rtp entry 2. Created an .hdb entry 3. Defined all nonbonded parameters for new atomtypes in the .atp and ffnonbonded.itp file 4. Defined all new bonded parameters in ffbonded.itp I think you need to define CRO as Protein in residuetypes.dat so that the pdb2gmx mechanism can deduce that it should form a C-terminal peptide link in the absence of an end-of-chain marker. Similarly, I have a modified peptide in what's become my system for generating pdb2gmx bugzilla reports, and with 4.5.1 and git head, if I omit the residuetypes.dat definition I see Identified residue ALA1 as a starting terminus. Warning: Residue KCX193 in chain has different type (Other) from starting residue ALA1 (Protein). Warning: Residue ASP194 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASP195 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue GLU196 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASN197 in chain has different type (Protein) from starting residue ALA1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue THR192 as a ending terminus. snip --- Program pdb2gmx_master, VERSION 4.5.1-20100916-6d51340 Source code file: ../../../src/kernel/pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue VAL 467 was not found in rtp entry VAL with 16 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- This is a bit different, inasmuch as I see the error on the final residue of the first chain, rather then on the modified residue, as you do. However pdb2gmx should cope better with this case - clearly it's confused in the above messages about non-matching types. We should probably file a bugzilla, even if this fixes your symptoms. Mark The coordinate file was then input into pdb2gmx with an oplsaa.ff directory in the working directory. I received the following error (identical with version 4.5 and the most recent git with release-4-5-patches): pdb2gmx -f struct.pdb ... --- Program pdb2gmx, VERSION 4.5.1-20100920-03d181e Source code file: pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue CRO 331 was not found in rtp entry CRO with 39 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The CRO residue is my chromophore. I'm wondering why pdb2gmx is finding an OXT atom in the following coordinates: ... ATOM 2528 N LEU A 330 -13.640 10.888 -25.907 1.00 0.00 ATOM 2529 CA LEU A 330 -12.513 11.013 -26.852 1.00 0.00 ATOM 2530 C LEU A 330 -11.281 10.183 -26.416 1.00 0.00 ATOM 2531 O LEU A 330 -10.625 9.588 - 27.277 1.00 0.00 ATOM 2532 CB LEU A 330 -12.159 12.493 -27.066 1.00 0.00 ATOM 2533 CG LEU A 330 -13.206 13.415 -27.691 1.00 0.00 ATOM 2534 CD1 LEU A 330 -12.913 14.905 -27.393 1.00 0.00 ATOM 2535 CD2 LEU A 330 -13.400 13.160 -29.207 1.00 0.00 ATOM 2536 N CRO A 331 -10.669 9.142 - 25.611 1.00 0.00 ATOM 2537 CE CRO A 331 -7.407 12.564 - 27.240 1.00 0.00 ATOM 2538 SD CRO A 331 -8.035 12.603 - 25.595 1.00 0.00 ATOM 2539 CG1 CRO A 331 -8.731 10.996 - 25.519 1.00 0.00 ATOM 2540 CB1 CRO A 331 -9.618 10.846 - 24.279 1.00 0.00 ATOM 2541 CA1 CRO A 331 -10.227 9.470 - 24.406 1.00 0.00 ATOM 2542 C1 CRO A 331 -10.304 8.516 - 23.260 1.00 0.00 ATOM 2543 N2 CRO A 331 -9.873 8.765 - 21.981 1.00 0.00 ATOM 2544 OH CRO A 331 -8.594 11.111 - 15.969 1.00 0.00 ATOM 2545 CD2 CRO A 331 -9.219 9.756 - 19.205 1.00 0.00 ATOM 2546 CE2 CRO A 331 -8.888 10.677 - 18.207 1.00 0.00 ATOM 2547 CZ CRO A 331 -8.898 10.286 - 16.863 1.00 0.00 ATOM 2548 CE1 CRO A 331 -9.219 8.975 - 16.518 1.00 0.00 ATOM 2549 CD1 CRO A 331 -9.549 8.056 - 17.509 1.00 0.00 ATOM 2550 CG2
Re: [gmx-users] Problem with pdb2gmx and a new residue
Mark Abraham wrote: - Original Message - From: Justin A. Lemkul jalem...@vt.edu Date: Tuesday, September 21, 2010 6:30 Subject: [gmx-users] Problem with pdb2gmx and a new residue To: Gromacs Users' List gmx-users@gromacs.org Hi All, I'm trying to build a topology for a chromophore-containing protein using Gromacs 4.5 and OPLS-AA. The chromophore is incorporated into the protein's backbone and the parameters all come from a reputable publication, so I've done the following: 1. Created a new .rtp entry 2. Created an .hdb entry 3. Defined all nonbonded parameters for new atomtypes in the .atp and ffnonbonded.itp file 4. Defined all new bonded parameters in ffbonded.itp I think you need to define CRO as Protein in residuetypes.dat so that the pdb2gmx mechanism can deduce that it should form a C-terminal peptide link in the absence of an end-of-chain marker. I had done that, I forgot to mention it. I tried using my modified residuetypes.dat from both the working directory and in $GMXLIB. Similarly, I have a modified peptide in what's become my system for generating pdb2gmx bugzilla reports, and with 4.5.1 and git head, if I omit the residuetypes.dat definition I see Identified residue ALA1 as a starting terminus. Warning: Residue KCX193 in chain has different type (Other) from starting residue ALA1 (Protein). Warning: Residue ASP194 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASP195 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue GLU196 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASN197 in chain has different type (Protein) from starting residue ALA1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue THR192 as a ending terminus. snip --- Program pdb2gmx_master, VERSION 4.5.1-20100916-6d51340 Source code file: ../../../src/kernel/pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue VAL 467 was not found in rtp entry VAL with 16 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- This is a bit different, inasmuch as I see the error on the final residue of the first chain, rather then on the modified residue, as you do. However pdb2gmx should cope better with this case - clearly it's confused in the above messages about non-matching types. We should probably file a bugzilla, even if this fixes your symptoms. I figured as much, just thought I'd check to see if I'd missed anything obvious. Thanks for the reply. I'll file a bugzilla. -Justin Mark The coordinate file was then input into pdb2gmx with an oplsaa.ff directory in the working directory. I received the following error (identical with version 4.5 and the most recent git with release-4-5-patches): pdb2gmx -f struct.pdb ... --- Program pdb2gmx, VERSION 4.5.1-20100920-03d181e Source code file: pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue CRO 331 was not found in rtp entry CRO with 39 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The CRO residue is my chromophore. I'm wondering why pdb2gmx is finding an OXT atom in the following coordinates: ... ATOM 2528 N LEU A 330 -13.640 10.888 -25.907 1.00 0.00 ATOM 2529 CA LEU A 330 -12.513 11.013 -26.852 1.00 0.00 ATOM 2530 C LEU A 330 -11.281 10.183 -26.416 1.00 0.00 ATOM 2531 O LEU A 330 -10.625 9.588 - 27.277 1.00 0.00 ATOM 2532 CB LEU A 330 -12.159 12.493 -27.066 1.00 0.00 ATOM 2533 CG LEU A 330 -13.206 13.415 -27.691 1.00 0.00 ATOM 2534 CD1 LEU A 330 -12.913 14.905 -27.393 1.00 0.00 ATOM 2535 CD2 LEU A 330 -13.400 13.160 -29.207 1.00 0.00 ATOM 2536 N CRO A 331 -10.669 9.142 - 25.611 1.00 0.00 ATOM 2537 CE CRO A 331 -7.407 12.564 - 27.240 1.00 0.00 ATOM 2538 SD CRO A 331 -8.035 12.603 - 25.595 1.00 0.00 ATOM 2539 CG1 CRO A 331 -8.731 10.996 - 25.519 1.00 0.00 ATOM 2540 CB1 CRO A 331 -9.618 10.846 - 24.279 1.00 0.00 ATOM 2541 CA1 CRO A 331 -10.227 9.470 - 24.406 1.00 0.00 ATOM 2542 C1 CRO A 331 -10.304 8.516 - 23.260 1.00 0.00 ATOM 2543 N2 CRO A 331 -9.873 8.765 - 21.981 1.00 0.00 ATOM 2544 OH CRO A 331 -8.594 11.111 - 15.969 1.00 0.00 ATOM
Re: [gmx-users] error on compilation on BlueGene/P
Hi, IIRC GROMACS has done something radical to FORTRAN inner loops (like removing them) since those instructions were written. Removing --enable-fortran will make your symptoms go away. The C inner loops will be fine, should you ever be running mdrun on the front end nodes. ... and if I add the --enable-bluegene flag : ../../../../../src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_gen_bluegene.h, line 163.21: 1506-1231 (S) The built-in function __fpsub is not valid for the target architecture. and more similar errors. Sure. --enable-bluegene is only useful for the mdrun binary for the compute system. Mark On 09/20/2010 05:35 PM, Fabio Affinito wrote: Hi all, I'm trying to install Gromacs on BG/P following the instruction reported here: http://www.gromacs.org/Downloads/Installation_Instructions/GROMACS_on_BlueGene I ran configure: ../configure --prefix=/bgp/userinternal/cin0644a/gromacs \ --enable-ppc-sqrt \ --disable-ppc-altivec \ --enable-fortran \ --with-fft=fftw3 \ --without-x \ CFLAGS=-O3 -qarch=auto -qtune=auto \ CC=xlc_r -q64 \ CXX=xlC_r -q64 \ CXXFLAGS=-O3 -qarch=auto -qtune=auto \ CPPFLAGS=-I/bgp/userinternal/cin0644a/fftwlibs/include \ F77=xlf_r -q64 \ FFLAGS=-O3 -qnoprefetch -qarch=auto -qtune=auto \ LDFLAGS=-L/bgp/userinternal/cin0644a/fftwlibs/lib But when I compile with make I get this error: ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 42.10: 1506-296 (S) #include file nbkernel010_f77_single.h not found. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 43.10: 1506-296 (S) #include file nbkernel020_f77_single.h not found. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 44.10: 1506-296 (S) #include file nbkernel030_f77_single.h not found. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 45.10: 1506-296 (S) #include file nbkernel100_f77_single.h not found. [...] ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 114.5: 1506-045 (S) Undeclared identifier nbkernel010_f77_single. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 115.5: 1506-045 (S) Undeclared identifier nbkernel020_f77_single. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 116.5: 1506-045 (S) Undeclared identifier nbkernel030_f77_single. ../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c, line 117.5: 1506-045 (S) Undeclared identifier nbkernel100_f77_single. Do you have any hint about that? Thanks in advance! F. -- * Fabio Affinito, PhD CINECA InterUniversity Computer Center Via Magnanelli, 6/3 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) e-mail: f.affin...@cineca.it -- 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] creating a solvent box
This may very well be a simple problem, but I have found little in the way of documentation that helped me get it to work: I'd like to form a box (4x6x4 nm^3) filled with 3200 water molecules. I'd like to use the water model specified in sw.itp (polarizable flexible). In the working directory I have a pdb file that specifies exactly the final system that I want to use, but I cannot generate a .gro file from this pdb file in order to run a simulation. I've tried 2 routes to accomplish this: 1) pdb2gmx - I've attempted to use this program as follows: 'pdb2gmx_d -f sw_box.pdb -o sw_box.gro -i sw.itp' This reports a fatal error: Residue 'SW' not found in residue topology database Because the sw.itp file defines SW as the molecule name, and again as the residue name, I assumed that's what I'd want to appear in my pdb file as well. I've tried every combination of force fields and water model to see if that would do anything, but to no avail. 2) genbox - I tried to generate a solvent box using the pdb file as the solvent definition: 'genbox_d -cs sw_box.pdb -box 4.0 6.0 4.0 -maxsol 3200' This made it look as though it was running, but after a very long time it did not return and produce a .gro file I could use. It's as if the program just hung or got stuck in some overly complicated solvation routine. I realize that the SW residue is not defined in the standard force fields, and so that's why I want to include sw.itp. Is there a way to generate this box? -- 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] creating a solvent box
Eric Shamay wrote: This may very well be a simple problem, but I have found little in the way of documentation that helped me get it to work: I'd like to form a box (4x6x4 nm^3) filled with 3200 water molecules. I'd like to use the water model specified in sw.itp (polarizable flexible). In the working directory I have a pdb file that specifies exactly the final system that I want to use, but I cannot generate a .gro file from this pdb file in order to run a simulation. I've tried 2 routes to accomplish this: 1) pdb2gmx - I've attempted to use this program as follows: 'pdb2gmx_d -f sw_box.pdb -o sw_box.gro -i sw.itp' This reports a fatal error: Residue 'SW' not found in residue topology database Because the sw.itp file defines SW as the molecule name, and again as the residue name, I assumed that's what I'd want to appear in my pdb file as well. I've tried every combination of force fields and water model to see if that would do anything, but to no avail. Since you've already got sw.itp, then there's no point at all in running pdb2gmx, whose sole purpose is to create topologies. Since you've got that, your life should be easy: #include (force field) #include sw.itp [ system ] SW [ molecules ] SW 3200 2) genbox - I tried to generate a solvent box using the pdb file as the solvent definition: 'genbox_d -cs sw_box.pdb -box 4.0 6.0 4.0 -maxsol 3200' This made it look as though it was running, but after a very long time it did not return and produce a .gro file I could use. It's as if the program just hung or got stuck in some overly complicated solvation routine. I realize that the SW residue is not defined in the standard force fields, and so that's why I want to include sw.itp. Is there a way to generate this box? Above you state that sw_box.pdb contains the system you want. If that's the case, there's no need for genbox at all. Use sw_box.pdb as your coordinate file input into grompp in conjunction to the skeleton topology I have shown above. If your goal is simply to obtain a .gro file, just use editconf. But do note that there is no requirement whatsoever that you have to use .gro format. Most Gromacs tools are extremely flexible, and a .pdb file will work just fine. -Justin -- 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] creating a solvent box
Is there something about the water molecule that is different to any standard H2O? If not, then simply use: genbox_d -cs -box 4.0 6.0 4.0 -maxsol 3200 Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9909 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Eric Shamay Sent: Tuesday, 21 September 2010 10:17 AM To: gmx-users@gromacs.org Subject: [gmx-users] creating a solvent box This may very well be a simple problem, but I have found little in the way of documentation that helped me get it to work: I'd like to form a box (4x6x4 nm^3) filled with 3200 water molecules. I'd like to use the water model specified in sw.itp (polarizable flexible). In the working directory I have a pdb file that specifies exactly the final system that I want to use, but I cannot generate a .gro file from this pdb file in order to run a simulation. I've tried 2 routes to accomplish this: 1) pdb2gmx - I've attempted to use this program as follows: 'pdb2gmx_d -f sw_box.pdb -o sw_box.gro -i sw.itp' This reports a fatal error: Residue 'SW' not found in residue topology database Because the sw.itp file defines SW as the molecule name, and again as the residue name, I assumed that's what I'd want to appear in my pdb file as well. I've tried every combination of force fields and water model to see if that would do anything, but to no avail. 2) genbox - I tried to generate a solvent box using the pdb file as the solvent definition: 'genbox_d -cs sw_box.pdb -box 4.0 6.0 4.0 -maxsol 3200' This made it look as though it was running, but after a very long time it did not return and produce a .gro file I could use. It's as if the program just hung or got stuck in some overly complicated solvation routine. I realize that the SW residue is not defined in the standard force fields, and so that's why I want to include sw.itp. Is there a way to generate this box? -- 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] Problem with pdb2gmx and a new residue
Hi Justin, Presently i too facing the same exact problem. I built the topology for a chromophore in the protein and entered all the new parameters in the .rtp, atp, hdb and defined the bonded and nonbonded parameters. Finally i got the following error. Fatal error: Atom OXT in residue CRIH 64 was not found in rtp entry CRIH with 27 atoms while sorting atoms. By this time if you identified the problem. Please help me too. Thank you. Rama On Mon, Sep 20, 2010 at 3:00 PM, Justin A. Lemkul jalem...@vt.edu wrote: Mark Abraham wrote: - Original Message - From: Justin A. Lemkul jalem...@vt.edu Date: Tuesday, September 21, 2010 6:30 Subject: [gmx-users] Problem with pdb2gmx and a new residue To: Gromacs Users' List gmx-users@gromacs.org Hi All, I'm trying to build a topology for a chromophore-containing protein using Gromacs 4.5 and OPLS-AA. The chromophore is incorporated into the protein's backbone and the parameters all come from a reputable publication, so I've done the following: 1. Created a new .rtp entry 2. Created an .hdb entry 3. Defined all nonbonded parameters for new atomtypes in the .atp and ffnonbonded.itp file 4. Defined all new bonded parameters in ffbonded.itp I think you need to define CRO as Protein in residuetypes.dat so that the pdb2gmx mechanism can deduce that it should form a C-terminal peptide link in the absence of an end-of-chain marker. I had done that, I forgot to mention it. I tried using my modified residuetypes.dat from both the working directory and in $GMXLIB. Similarly, I have a modified peptide in what's become my system for generating pdb2gmx bugzilla reports, and with 4.5.1 and git head, if I omit the residuetypes.dat definition I see Identified residue ALA1 as a starting terminus. Warning: Residue KCX193 in chain has different type (Other) from starting residue ALA1 (Protein). Warning: Residue ASP194 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASP195 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue GLU196 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ASN197 in chain has different type (Protein) from starting residue ALA1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue THR192 as a ending terminus. snip --- Program pdb2gmx_master, VERSION 4.5.1-20100916-6d51340 Source code file: ../../../src/kernel/pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue VAL 467 was not found in rtp entry VAL with 16 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- This is a bit different, inasmuch as I see the error on the final residue of the first chain, rather then on the modified residue, as you do. However pdb2gmx should cope better with this case - clearly it's confused in the above messages about non-matching types. We should probably file a bugzilla, even if this fixes your symptoms. I figured as much, just thought I'd check to see if I'd missed anything obvious. Thanks for the reply. I'll file a bugzilla. -Justin Mark The coordinate file was then input into pdb2gmx with an oplsaa.ff directory in the working directory. I received the following error (identical with version 4.5 and the most recent git with release-4-5-patches): pdb2gmx -f struct.pdb ... --- Program pdb2gmx, VERSION 4.5.1-20100920-03d181e Source code file: pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue CRO 331 was not found in rtp entry CRO with 39 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The CRO residue is my chromophore. I'm wondering why pdb2gmx is finding an OXT atom in the following coordinates: ... ATOM 2528 N LEU A 330 -13.640 10.888 -25.907 1.00 0.00 ATOM 2529 CA LEU A 330 -12.513 11.013 -26.852 1.00 0.00 ATOM 2530 C LEU A 330 -11.281 10.183 -26.416 1.00 0.00 ATOM 2531 O LEU A 330 -10.625 9.588 - 27.277 1.00 0.00 ATOM 2532 CB LEU A 330 -12.159 12.493 -27.066 1.00 0.00 ATOM 2533 CG LEU A 330 -13.206 13.415 -27.691 1.00 0.00 ATOM 2534 CD1 LEU A 330 -12.913 14.905 -27.393 1.00 0.00 ATOM 2535 CD2 LEU A 330 -13.400 13.160 -29.207 1.00 0.00 ATOM 2536 N CRO A 331 -10.669 9.142 - 25.611 1.00 0.00 ATOM 2537
RE: [gmx-users] Energy Minimzation with Gromacs leads to distortionof planar groups
Hi Thanks a lot for the suggestions. I removed -DFLEXIBLE this time but it still didn't work unfortunately. I started off with 0 distorted planar group and ended up with 38 after minimization (same as before). Justin, the values were as below when the minimization converged to machine precision Pot E= -1.6560090 e+04 (initial = 5.64598 e+09) Max force = 2.8172894 e+02 (initial = 7.95313 e+11) Norm of force = 2.9346647 e+01 HW -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Monday, September 20, 2010 7:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy Minimzation with Gromacs leads to distortionof planar groups Kukol, Andreas wrote: Try without -DFLEXIBLE. See this message: http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html Doesn't -DFLEXIBLE only affect water, not the aromatic rings of the protein? Don't the real problems come from running actual MD with -DFLEXBILE? In some cases for EM, it has even been recommended. -Justin Andreas --- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of NG HUI WEN Sent: 20 September 2010 04:21 To: gmx-users@gromacs.org Subject: [gmx-users] Energy Minimzation with Gromacs leads to distortion of planar groups Dear Gmxusers, I have noticed that energy minimization with gromacs (gromos G53a6 forcefield) had led to the distortion of sidechain planarity in my protein model. Comparison of PROCEHCK results between the pre- and post energy minimized structures have shown an increase in the number of distorted planar groups (e.g. rings and non-ring aliphatic groups). As steepest descent seem to converge very rapidly (500 steps) to machine precision, I also tried using the conjugate gradient and lbfgs methods. The .mdp files used are as follow. Steepest descent title = Energy Minimization without position restraint cpp = /lib/cpp ; Preprocessor define= -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps= 500 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple; Method to determine neighbor list (simple, grid) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off constraints = none; Bond types to replace by constraints pbc = no; Periodic Boundary Conditions (yes/no) CG title = Energy Minimization with out position restraint cpp = /lib/cpp ; Preprocessor define= -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = cg; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol dt = 0.0001 nsteps= 500 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple; Method to determine neighbor list (simple, grid) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off constraints = none; Bond types to replace by constraints pbc = no; Periodic Boundary Conditions (yes/no) lbfgs title = Energy Minimization without position restraint cpp = /lib/cpp ; Preprocessor define= -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = l-bfgs ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps= 1500; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple; Method to determine neighbor list (simple, grid) coulombtype = pme ;
[gmx-users] MD on docked complex using AMBER FF
Hi There, I am trying to run molecular dynamics on a drug-enzyme complex using amber force field. I have done it earlier using gromos FF using drug-enzyme tutorial, I dont know if the parameter set (.mdp file) will be same or different while using AMBER FF. Any insight/comments into the matter may be of help if somebody has tried using AMBER FF for docked complex in GROMACS. Thanks in advance. regards, Vivek -- 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] MD on docked complex using AMBER FF
First, you have to develop parameter for your molecule withing Amber. Then you have to create .prmtop and .inpcrd files for your molecule, and than you can convert the Amber topology to Gromacs topology. You will need AmberTools and a script called amb2gmx.pl. Following links would be helpful for you http://ambermd.org/#AmberTools http://ambermd.org/antechamber/efz.html ffamber.cnsm.csulb.edu/*amb2gmx*.*pl* On Tue, Sep 21, 2010 at 12:51 AM, vivek sharma viveksharma.i...@gmail.comwrote: Hi There, I am trying to run molecular dynamics on a drug-enzyme complex using amber force field. I have done it earlier using gromos FF using drug-enzyme tutorial, I dont know if the parameter set (.mdp file) will be same or different while using AMBER FF. Any insight/comments into the matter may be of help if somebody has tried using AMBER FF for docked complex in GROMACS. Thanks in advance. regards, Vivek -- 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
