[gmx-users] Fwd: Diffusion of protein
Hello all I am trying to performed molecular dynamics simulation of ligand-protein complex in popc lipid with charmm36 force field. I am taking help from Justin A. Lemkul tutorial. I wanted to calculate the diffusion of the protein. Before performing the study I removed the PBC of my system. I am using msd command *g_msd -f md_whole.xtc -s md.tpr -b 0 -e 10 -o diffusion.xvg* but the graph is not a straight line [image: Inline image 1] when I am using g_analyse after g_msd command i.e. *g_analyze -f diffusion.xvg -msd diffusion_analyze.xvg *the graph is straight line but the graph is showing only for 50 ns (half of the simulation time) Can anyone please tell me which graph should I refer. Or I am doing something wrong?? Is there any other command to calculate the diffusion? Please help With Regards Neha bharty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Swissparam itp file
Hello all I am trying to perform molecular dynamics simulation of ligand-protein complex in popc lipid with charmm36 force field. I am taking help from Justin A. Lemkul tutorial. First I perform orientation of protein ligand complex by following command: editconf -princ -f complex.gro -o complex_princ.gro editconf -rotate 0 90 0 -f complex_princ.gro -o complex_princ_rotate.gro Then after I separated the protein and ligand to generate their topology file. For protein pdb2gmx command is used for topology generation. For ligand topology file swissparam is used after adding the hydrogen and converting it to mol2 format. But from swissparam I only get the .par and .rtf file in zip folder and .itp is not persent. how to solve this issue?? Although when I use the ligand molecule without orientation (without performing editconf -princ and editconf -rotate command) swissparam gives the .itp file. Can I use this itp file for oriented ligand molecule?? Please help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Force field For Protein-Ligand Complex
Hello All I have to perform molecular dynamics simulation of protein-ligand complex in water. Initially I tried using gromos force field but there is some problem in its ligand itp file which is generated by PRODRG server. I also tried it with the help of ATB but again its giving error. Can I use CHARMM 27 or Charmm 36 force field for the same. Is there any reference paper?? Please help. With Regards Neha Bharti -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Error during NVT
constraints from all_bond to h-bonds it run successfully. Is this a correct way?? Following are my em.mdp and nvt.mdp file : EM.mdp file: title= Minimization; Title of run ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform energygrps= Protein <0> ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.0; long range electrostatic cut-off rvdw= 1.0; long range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions NVT.mdp file: title = Protein-ligand complex NVT equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md; leap-frog integrator nsteps = 100 ; 2 * 100 = 2000 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 nstvout = 500 nstenergy = 500 nstlog = 500 energygrps = Protein <0> ; Bond parameters continuation = no constraint_algorithm = lincs constraints = h-bonds lincs_iter = 1 lincs_order = 4 ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet rcoulomb= 1.4 ; short-range electrostatic cutoff (in nm) rlist = 1.4 rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_<0> Water_and_ions; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed Please Help. With Regards Neha Bharti -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Ligand Topology file
Hello All I am performing Molecular dynamics simulation of protein and ligand complex. I am using GROMOS96 53a6 force field. For Ligand topology file I am using Automated topology builder. In the grompp step ( grompp -f ion.mdp -c solv.gro -p topol.top -o ions.tpr) when I tried to add ion it gives me Note that NOTE 2 [file topol.top]: The largest charge group contains 14 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Following is the atom charge group of .itp file which I get from Automated topology builder [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1 C 16P5PC151 -0.050 12.0110 2 C 16P5PC1610.023 12.0110 3 C 16P5PC1710.023 12.0110 4 C 16P5PC181 -0.050 12.0110 5 C 16P5PC1910.023 12.0110 6 C 16P5PC2010.023 12.0110 7 C 16P5PC1410.580 12.0110 8 O 16P5P O1 1 -0.571 15.9994 9 C 16P5PC2110.570 12.0110 10 O 16P5P O21 -0.571 15.9994 ; 0.000 11 N 16P5P N32 -0.486 14.0067 12 H 16P5PH1120.486 1.0080 ; 0.000 13 C 16P5PC1230.251 12.0110 14 C 16P5PC113 -0.019 12.0110 15 C 16P5PC103 -0.070 12.0110 16 C 16P5P C930.089 12.0110 17 C 16P5P C83 -0.185 12.0110 18 C 16P5PC133 -0.089 12.0110 19 C 16P5P C730.491 12.0110 20NR16P5P N23 -0.468 14.0067 ; -0.000 21NR16P5P N14 -0.365 14.0067 22 H 16P5P H140.365 1.0080 ; 0.000 23 C 16P5P C550.155 12.0110 24 C 16P5P C450.115 12.0110 25 C 16P5P C65 -0.042 12.0110 26 C 16P5P C35 -0.042 12.0110 27 C 16P5P C25 -0.093 12.0110 28 C 16P5P C15 -0.093 12.0110 ; 0.000 29 N 16P5P N46 -0.486 14.0067 30 H 16P5PH1660.486 1.0080 ; 0.000 31 C 16P5PC2270.240 12.0110 32 C 16P5PC277 -0.100 12.0110 33 C 16P5PC267 -0.196 12.0110 34 C 16P5PC2570.078 12.0110 35 C 16P5PC247 -0.081 12.0110 36 C 16P5PC237 -0.030 12.0110 37 C 16P5PC2870.478 12.0110 38NR16P5P N67 -0.475 14.0067 39 C 16P5PC3470.138 12.0110 40 C 16P5PC2970.170 12.0110 41 C 16P5PC337 -0.030 12.0110 42 C 16P5PC307 -0.030 12.0110 43 C 16P5PC317 -0.081 12.0110 44 C 16P5PC327 -0.081 12.0110 ; 0.000 45NR16P5P N58 -0.365 14.0067 46 H 16P5P H280.365 1.0080 ; 0.000 ; total charge of the molecule: -0.000 Should I ignore the error or is there something wrong in my charge group generated from ATB. Can any one please help me out to solve the problem. Thanks You. With Regards Neha Bharti -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Implicit and explicit solvation
Hello all Can any one please tell me What is Implicit and explicit solvation?? And Which kind of solvation is used in Justin A. Lemkul tutorial?? With Regards Neha bharty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Force Field for protein in water
Hello All I am trying to MD simulation of protein in water and same Protein bound with Ligand in water. Which force field is good for both the cases. I just want to compare the results of bound and unbound Proteins. So, Should I use different force fields for both or same force field. Please Help. With Regards Neha Bharty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Different fluctuation after concatenation
Hello All I am trying to perform Molecular dynamics simulation for protein ligand complex in popc lipid with charmm36 force field. Initially my run was of 50ns then I extended by run to 100ns. The first 50ns run is done in two phase (30ns and 20ns) using cpt file as there is time limit in supercomputer. then I concatenate both the .trr files using trjcat -f md_0_1.trr md_0_2.trr -o md.trr After that I extend my run to 75ns and concatenate trr file with 50ns file then again I extend the run to 100ns and perform the same concatenation step. the tpr file is extended using tpbconv -s input_md.tpr -o input_md_extended.tpr -extend 25000 I individually saw the fluctuation of all the trr using VMD. And after that I also visualize the fluctuation of final concatenated file using last 100ns .gro using VMD. I found in my individual files the fluctuation of ligand is different as compare to the final one. So the concatenation of trr file is not proper what is the reason. Please Help With Regards Neha Bharty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Ligand is not in the same position as in PDB file
Thank you very much mark for your reply. I merge the protein and ligand file before starting the molecular dynamics simulation. Then I start the MD run. I don't how to post-process the output. can you please tell me how to perform it or is there any article or tutorial available for that. Thanks and regards Neha Bharty >Hi, >Probably you are seeing normal behaviour in the presence of >http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions <http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions> . >If you want to visualize the protein and ligand as a complex, you need to >post-process the output accordingly. mdrun doesn't know that you plan to >treat them as special. >Mark >On Tue, Nov 11, 2014 at 9:50 AM, neha bharti >wrote: >> Hello All >> >> I am trying to perform MD for protein-ligand complex in popc lipid with >> charmm36 force field and also follow Justin A. Lemkul tutorial. >> I downloaded the pdb structure of protein and ligand complex and the >> separate the protein and ligand file and prepare the system. >> >> Finally I perform the MD run for 100 ns, I found that the ligand is not in >> the same place as present in PDB file of protein ligand complex. >> >> Is it necessary that the protein should be in the same position as present >> in protein ligand complex PDB file ?? >> >> Is there something wrong in my work. >> >> Please Help. >> >>Thanks and regard -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Ligand is not in the same position as in PDB file
Hello All I am trying to perform MD for protein-ligand complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I downloaded the pdb structure of protein and ligand complex and the separate the protein and ligand file and prepare the system. Finally I perform the MD run for 100 ns, I found that the ligand is not in the same place as present in PDB file of protein ligand complex. Is it necessary that the protein should be in the same position as present in protein ligand complex PDB file ?? Is there something wrong in my work. Please Help. Thanks and regards Neha Bharty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to mearg Ligand protein and Lipid
Hello All I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I also wanted to ask that while create special index groups consisting of solvent + ions and protein + lipids using make_ndx if i am having a system with ligand molecule also then should I add it with protein lipid complex or add it separately with protein like 16 | 14" to merge the SOL and CL groups "1 | 13 |" to merge Protein and POPC groups and 1 | 12 to merge Protein and LIGAND groups or I can add them like 1 | 12 | 13 to merge Protein and LIGAND and POPC groups With Regards Neha bharty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization problem after editconf step
Thanks for your reply Justin The error is now solve but I don't know this is a right way or not. The step which I perform previously in which I am facing error: Packing : 1) perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat 2) grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr 3) mdrun -v -deffnm em I did this till 24 iteration then I reached area per lipid 0.70 nm^2 4) Adding Solvent: a) editconf -f system_shrink.gro -o POPC_box.gro -box 8.68740 8.41864 12.70145 b) genbox -cp POPC_box.gro -cs spc216.gro -o POPC_sol.gro 5) Adding Ions a) grompp -f ion.mdp -c POPC_sol.gro -p topol.top -o ion.tpr b) genion -s ion.tpr -o POPC_sol_ions.gro -p topol.top -pname NA -np 1 -nname CL Select 16 to add 1 possitive ion to sol 6) Energy Minimization Next, energy minimize the entire system now, using the following commands: a) grompp -f em.mdp -c POPC_sol_ions.gro -p topol.top -o em.tpr b) mdrun -v -deffnm em In energy minimization step The following error occur Steepest Descents converged to machine precision in 18 steps, but did not reach the requested Fmax < 1000. Potential Energy = 6.1499341e+20 Maximum force =inf on atom 3300 Norm of force = 5.4206209e+1 But if I skip the editconf step 4(a) the the energy minimization is normal. But i need to increase the box size because my protein is out of the box. So I did some changes before the packing which gives the correct result. The steps are as follows: Before energy minimization of POPC.gro I remove the water (SOL molecule manually) then increase the box size by 1) editconf -f POPC.gro -o popc_new.gro -box 8.68740 8.41864 15 : With the help of this command I increase the box size of popc.gro which I have downloaded. ( Peter C. Lai POPC lipid http://cesium.hyperfine.info/~peter /gromacs/popc36/ ) 2) genbox -cp POPC_new.gro -cs spc216.gro -o POPC_new_sol.gro : Add solvent 3) Energy minimization: a) grompp -f em.mdp -c POPC_new_sol.gro -p topol_popc.top -o em.tpr b) mdrun -v -deffnm em 4) trjconv to remove periodicity: trjconv -s em.tpr -f em.gro -o popc_whole.gro -pbc mol -ur compact select 0 for system orient the KALP peptide within this same coordinate frame as popc_whole.gro editconf -f conf.gro -o conf_newbox.gro -c -box 8.68740 8.41864 12.70145 Rest of the step is same as above after packing I took system_shrink24.gro without using editconf because I already arrange the size of the box like Adding Solvent: a) genbox -cp system_shrink24.gro -cs spc216.gro -o POPC_sol.gro Adding Ions a) grompp -f ion.mdp -c POPC_sol.gro -p topol.top -o ion.tpr b) genion -s ion.tpr -o POPC_sol_ions.gro -p topol.top -pname NA -np 1 -nname CL Select 16 to add 1 possitive ion to sol 6) Energy Minimization Next, energy minimize the entire system now, using the following commands: a) grompp -f em.mdp -c POPC_sol_ions.gro -p topol.top -o em.tpr b) mdrun -v -deffnm em When I perform by above method my energy minimization occur. Is this the right way?? Thanks With Regards Neha bharty > > Hello All >> >> I am trying to perform MD for protein ligand complex in popc lipid with >> Charmm36 force field. I follow Justin A. Lemkul tutorial of membrane >> protein simulation. >> > > I have successfully perform till InflateGRO followed by energy minimization > > step. >> > > perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat >> > > grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr >> >> mdrun -v -deffnm em >> > > till 24 iteration then I reached area per lipid 0.70 nm^2 >> >> when I visualize the molecule then the box size small in Z axis so in >> editconf step I increase the box size and then add solvent and ion . when I >> increase the box size with editconf then there is atomic clashes occur.and >> giving following error: >> >> Steepest Descents converged to machine precision in 18 steps, > > but did not reach the requested Fmax < 1000. > > Potential Energy = 6.1499341e+20 > > Maximum force =inf on atom 3300 > >Norm of force = 5.4206209e+1 > >> >> When I skip this step (editconf) then the minimization is normal. >> But I need to increase the box size. >> How to increase the box size? > >You need to provide the exact commands that you used when manipulating the box, >otherwise it's pure guesswork. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy minimization problem after editconf step
Hello All I am trying to perform MD for protein ligand complex in popc lipid with Charmm36 force field. I follow Justin A. Lemkul tutorial of membrane protein simulation. I have successfully perform till InflateGRO followed by energy minimization step. perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr mdrun -v -deffnm em till 24 iteration then I reached area per lipid 0.70 nm^2 when I visualize the molecule then the box size small in Z axis so in editconf step I increase the box size and then add solvent and ion . when I increase the box size with editconf then there is atomic clashes occur.and giving following error: Steepest Descents converged to machine precision in 18 steps, but did not reach the requested Fmax < 1000. Potential Energy = 6.1499341e+20 Maximum force =inf on atom 3300 Norm of force = 5.4206209e+1 When I skip this step (editconf) then the minimization is normal. But I need to increase the box size. How to increase the box size? Please help With Regards Neha bharty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Atomic Clashes during Energy minimization
I am trying to perform MD for protein ligand complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I have created protein ligand complex as mention in Justin A. Lemkul Protein-Ligand Complex tutorial till Build the Topology Step. Then I perform The following Steps where I get error: Before Running InflateGRO I have separated the ligand and protein file because InflateGRO not deal with 1) InflateGRO script run: perl inflategro.pl system.gro 4 POPC 0 system_inflated.pdb 5 area.dat 2) Next is energy minimize grompp -f em.mdp -c system_inflated.gro -p topol.top -o em.tpr mdrun -v -deffnm em another script command: perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat Another energy minimization step: grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr mdrun -v -deffnm em Repeat this step. area per lipid reached 0.68 nm^2. Then I stop. 3) then again include the Ligand to final system_shrink.gro file 4) Adding Solvent: editconf -f system_shrink.gro -o POPC_box.gro -box 8 8 15 genbox -cp POPC_box.gro -cs spc216.gro -o POPC_sol.gro 5) Adding Ions Change topology.top file as numbers of SOL and ligand is added Now, neutralize the system by adding the proper number of counter-ions using: a) grompp -f ion.mdp -c POPC_sol.gro -p topol.top -o ion.tpr b) genion -s ion.tpr -o POPC_sol_ions.gro -p topol.top -pname NA -np 3 -nname CL Select 16 to add 3 positive ion to sol. 6) Energy Minimization Next, energy minimize the entire system now, using the following commands: a) grompp -f em.mdp -c POPC_sol_ions.gro -p topol.top -o em.tpr b) mdrun -v -deffnm em While preforming energy minimization step (mdrun -v -deffnm em) Atomic Clashes occur. And it give following output: Steepest Descents converged to machine precision in 18 steps, but did not reach the requested Fmax < 1000. Potential Energy = 6.1499341e+20 Maximum force =inf on atom 3300 Norm of force = 5.4206209e+1 I guess This is because of the ligand is removed before running InflateGRO, then added once the system is properly compressed. Then I also tried this by without Adding Ligand molecule but it* still giving the error* What to do to solve this issue?? When to add the ligand to the system?? Please Help.. With Regards Neha bharty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Missing Residues of PDB file
Hello Rama david Thank you very much for your reply. The residue is missing from the middle as well as from the end. Hence I have modeled it with the help of homology modeling. Then I align both the protein (PDB downloaded as well as homology modelled) and get a RMSD fluctuation of 0.45 with the help of pymol. My Method is correct or not?? Please Help Thank you very much. With regards Neha bharty >Dear Neha, > the question depend on which residue is missing?? >Is the residue is from middle or from end that is important. >If end residue is missing then no issue. but middle residue is problematic. >you can model the protein and then align it with pymol align command or any >other visualizing software. >With beat regards, >Rama david. On Mon, Aug 25, 2014 at 11:01 AM, RINU KHATTRI wrote: > use -missing in last of command pdb2gmx > > On Mon, Aug 25, 2014 at 10:54 AM, neha bharti > wrote: > > Hello All > > > > I am performing Molecular dynamics simulation of protein-ligand complex > > using charmm36 force field in popc lipid. > > > > I downloaded the protein ligand complex pdb file. And as mentioned in > > Justin A. Lemkul protein-ligand complex tutorial I have seperate ligand > and > > protein from pdb file. > > > > My protein contain some missing residues so I have homology modeled the > > protein taking the same pdb file as target and templet. > > > > At the time of Building the complex step I am using the homology modelled > > protein. > > > > Can I add the ligand in that file as shown in tutorial: > > > > 163ASN C 1691 0.621 -0.740 -0.126 > > 163ASN O1 1692 0.624 -0.616 -0.140 > > 163ASN O2 1693 0.683 -0.703 -0.011 > > 1JZ4 C4 1 2.429 -2.412 -0.007 > > 1JZ4 C14 2 2.392 -2.470 -0.139 > > 1JZ4 C13 3 2.246 -2.441 -0.181 > > 1JZ4 C12 4 2.229 -2.519 -0.308 > > 1JZ4 C11 5 2.169 -2.646 -0.295 > > > > because due to homology modeling it might be possible that the > coordinates > > of the protein will get change?? > > > > Or I should use maxwarn option to avoid the error message of missing > > residues of protein pdb file and no need of homology modelling?? > > > > Please Help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Missing Residues of PDB file (rama david)
Hello Rama david Thank you very much for your reply. The residue is missing from the middle as well as from the end. Hence I have modeled it with the help of homology modeling. Then I align both the protein (PDB downloaded as well as homology modelled) and get a RMSD fluctuation of 0.45 with the help of pymol. My Method is correct or not?? Please Help Thank you very much. With regards Neha bharty >Dear Neha, > the question depend on which residue is missing?? >Is the residue is from middle or from end that is important. >If end residue is missing then no issue. but middle residue is problematic. >you can model the protein and then align it with pymol align command or any >other visualizing software. >With beat regards, >Rama david. On Mon, Aug 25, 2014 at 11:01 AM, RINU KHATTRI wrote: > use -missing in last of command pdb2gmx > > On Mon, Aug 25, 2014 at 10:54 AM, neha bharti > wrote: > > Hello All > > > > I am performing Molecular dynamics simulation of protein-ligand complex > > using charmm36 force field in popc lipid. > > > > I downloaded the protein ligand complex pdb file. And as mentioned in > > Justin A. Lemkul protein-ligand complex tutorial I have seperate ligand > and > > protein from pdb file. > > > > My protein contain some missing residues so I have homology modeled the > > protein taking the same pdb file as target and templet. > > > > At the time of Building the complex step I am using the homology modelled > > protein. > > > > Can I add the ligand in that file as shown in tutorial: > > > > 163ASN C 1691 0.621 -0.740 -0.126 > > 163ASN O1 1692 0.624 -0.616 -0.140 > > 163ASN O2 1693 0.683 -0.703 -0.011 > > 1JZ4 C4 1 2.429 -2.412 -0.007 > > 1JZ4 C14 2 2.392 -2.470 -0.139 > > 1JZ4 C13 3 2.246 -2.441 -0.181 > > 1JZ4 C12 4 2.229 -2.519 -0.308 > > 1JZ4 C11 5 2.169 -2.646 -0.295 > > > > because due to homology modeling it might be possible that the > coordinates > > of the protein will get change?? > > > > Or I should use maxwarn option to avoid the error message of missing > > residues of protein pdb file and no need of homology modelling?? > > > > Please Help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Missing Residues of PDB file
Hello All I am performing Molecular dynamics simulation of protein-ligand complex using charmm36 force field in popc lipid. I downloaded the protein ligand complex pdb file. And as mentioned in Justin A. Lemkul protein-ligand complex tutorial I have seperate ligand and protein from pdb file. My protein contain some missing residues so I have homology modeled the protein taking the same pdb file as target and templet. At the time of Building the complex step I am using the homology modelled protein. Can I add the ligand in that file as shown in tutorial: 163ASN C 1691 0.621 -0.740 -0.126 163ASN O1 1692 0.624 -0.616 -0.140 163ASN O2 1693 0.683 -0.703 -0.011 1JZ4 C4 1 2.429 -2.412 -0.007 1JZ4 C14 2 2.392 -2.470 -0.139 1JZ4 C13 3 2.246 -2.441 -0.181 1JZ4 C12 4 2.229 -2.519 -0.308 1JZ4 C11 5 2.169 -2.646 -0.295 because due to homology modeling it might be possible that the coordinates of the protein will get change?? Or I should use maxwarn option to avoid the error message of missing residues of protein pdb file and no need of homology modelling?? Please Help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem in Ligand-Protein complex in POPC
Hello Justin Thank you very much for your help. You have asked me that "Are the coordinates of lig.pdb identical to those of lig_princ_rotate.pdb?" The coordinates are not exactly the same. There is some variations. I have also check by some modifications in my steps like First I separate protein and ligand molecule (protein.pdb and ligand.pdb) and convert the ligand.pdb to ligand.mol2 as mention in SwissParam site. then generating pdb and itp file for ligand.mol2 (lig.pdb and lig.itp) from SwissParam then combine lig.pdb with protein file and then rotate it. But in this case also the coordinates of ligand.pdb and lig.pdb (file generated from SwissParam) is little bit different in decimal poins The following residues were different: ligand.pdb: 31 H032 lig A120 47.750 2.557 46.295 1.00 0.00 SwissParam: 31 H032 LIG 1 47.750 2.558 46.295 1.00 0.00 ligand.pdb: 35 H06 lig A120 50.798 8.692 47.839 1.00 0.00 SwissParam: 35 H06 LIG 1 50.798 8.692 47.839 1.00 0.00 ligand.pdb: 42 H133 lig A120 49.687 7.251 46.290 1.00 0.00 SwissParam: 42 H133 LIG 1 49.688 7.251 46.290 1.00 0.00 ligand.pdb: 45 H16 lig A120 47.131 3.806 48.240 1.00 0.00 SwissParam: 45 H16 LIG 1 47.131 3.805 48.240 1.00 0.00 ligand.pdb: 60 H261 lig A120 49.641 3.735 45.830 1.00 0.00 SwissParam: 60 H261 LIG 1 49.641 3.735 45.831 1.00 0.00 ligand.pdb: 61 H262 lig A120 50.356 5.354 46.021 1.00 0.00 SwissParam: 61 H262 LIG 1 50.355 5.354 46.021 1.00 0.00 Can I use this file?? I also did a change in --- editconf -rotate 0 0 90 to editconf -rotate 0 90 0 because in when I rotate like -rotate 0 0 90 its parallel to lipid which was wrong. On 8/12/14, 6:50 AM, neha bharti wrote: >> Thank you very much justin for your reply. >> >> But I am still facing the problem to include ligand in protein. >> >> Following step I am performing: >> >> >> PDB file of protein complex with ligand is taken from pdb >> then >> >> 1) editconf -princ -f protein.pdb -o protein_princ.pdb >> >> 2) editconf -rotate 0 0 90 -f protein_princ.pdb -o protein_princ_rotate.pdb >> >> >> 3) separate protein and ligand files from protein_princ_rotate and then save >> then in different files >> >> protein file: protein_princ_rotate.pdb >> >> ligand file: lig_princ_rotate.pdb >> >> >> >> 4) generating pdb and itp file for small molecule >>lig.pdb >>lig.itp >> >Are the coordinates of lig.pdb identical to those of lig_princ_rotate.pdb? >> >> 5) Generation of topology files for protein: >> >> pdb2gmx -f protein_princ_rotate.pdb -water tip3p -ignh -o protein.pdb >> -nochargegrp >> >> >> 6) mearge protein.pdb and lig.pdb file in conf.pdb file >> >> >> 7) copy the files (mention in tutorial) from charmm36 force field and place >> them in new created folder charmm36_lipid.ff >> >> >> 8) Next, create a forcefield.doc file that contains a description of the >> force field parameters in it. Mine contains something like: >> >> CHARMM36 all-atom lipid force field (with CMAP), extended to include Berger >> lipid parameters >> >Don't do this! CHARMM36 and Berger are incompatible. CHARMM36 already >includes the lipid force field. >> >> 9) changes in topology file "charmm36/tip3p.itp" to >> "charmm36_lipid.ff/tip3p.itp" >> >> >> 10) Add Ligand Topology file: >> >> ; Include ligand topology >> #include "lig.itp" >> >> ; Include water topology >> #include "charmm36.ff/spc.itp" >> >Don't use SPC. It will re-define the water [moleculetype] and apply the wrong >parameters. Make sure you're using the CHARMM-specific TIP3P model (default in >the charmm36.ff package we provide). If you don't, the lipid force field will >produce bad results. >> 11) The next adjustment to be made is in the [ molecules ] directive. To >> account for the fact that there is a new molecule in conf.gro, we have to >> add it here, like so: >> >> [ molecules ] >> ; Compound#mols >> Protein_chain_A 1 >> LIG 1 >> >> download the following files: >> >> popc128a.pdb - the structure of a 128-lipid POPC bilayer >> popc.itp - the moleculetype definition POPC >> lipid.itp - Berger lipid parameters >> >You need an all-atom model of the lipid bilayer. CHARMM-GUI is a better source >of these coordinates. Don't use the united-atom Berger model from Peter >Tieleman in this cas
Re: [gmx-users] Problem in Ligand-Protein complex in POPC
Thank you very much justin for your reply. But I am still facing the problem to include ligand in protein. Following step I am performing: PDB file of protein complex with ligand is taken from pdb then 1) editconf -princ -f protein.pdb -o protein_princ.pdb 2) editconf -rotate 0 0 90 -f protein_princ.pdb -o protein_princ_rotate.pdb 3) separate protein and ligand files from protein_princ_rotate and then save then in different files protein file: protein_princ_rotate.pdb ligand file: lig_princ_rotate.pdb 4) generating pdb and itp file for small molecule lig.pdb lig.itp 5) Generation of topology files for protein: pdb2gmx -f protein_princ_rotate.pdb -water tip3p -ignh -o protein.pdb -nochargegrp 6) mearge protein.pdb and lig.pdb file in conf.pdb file 7) copy the files (mention in tutorial) from charmm36 force field and place them in new created folder charmm36_lipid.ff 8) Next, create a forcefield.doc file that contains a description of the force field parameters in it. Mine contains something like: CHARMM36 all-atom lipid force field (with CMAP), extended to include Berger lipid parameters 9) changes in topology file "charmm36/tip3p.itp" to "charmm36_lipid.ff/tip3p.itp" 10) Add Ligand Topology file: ; Include ligand topology #include "lig.itp" ; Include water topology #include "charmm36.ff/spc.itp" 11) The next adjustment to be made is in the [ molecules ] directive. To account for the fact that there is a new molecule in conf.gro, we have to add it here, like so: [ molecules ] ; Compound#mols Protein_chain_A 1 LIG 1 download the following files: popc128a.pdb - the structure of a 128-lipid POPC bilayer popc.itp - the moleculetype definition POPC lipid.itp - Berger lipid parameters 12) Orient the protein and membrane Convert the popc128.pdb to .gro format with editconf and remove the initial periodicity. (a) Generate a .tpr file for a popc-only system using grompp. grompp -f em.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr (b) Use trjconv to remove periodicity: trjconv -s em.tpr -f popc128a.pdb -o popc_whole.gro -pbc mol -ur compact select 0 for system 13) orient the peptide within this same coordinate frame as lipid, and place the center of mass of the peptide at the center of this box: editconf -f conf.gro -o conf_newbox.gro -c -box 6.23910 6.17970 6.91950 14) Pack the lipids around the protein and ligand complex First, concatenate the protein and bilayer structure files: cat conf_newbox.gro popc_whole.gro > system.gro 15) Remove unnecessary lines 16) Now, generate this new position restraint file using genrestr and include it in topology file: genrestr -f conf_newbox.gro -o strong_posre.itp -fc 10 10 10 select 0 for system 17)In the .mdp file used for the minimizations, add a line "define = -DSTRONG_POSRES" to make use of these new position restraints. 18) seperate the ligand and protein file because InflateGRO not deal with small molecule. then InflateGRO script run: perl inflategro.pl system.gro 4 POPC 0 system_inflated.pdb 5 area.dat 19) energy minimize: grompp -f em.mdp -c system_inflated.gro -p topol.top -o em.tpr mdrun -v -deffnm em another script command: perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat Another energy minimization step: grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr mdrun -v -deffnm em Repeat this step. area per lipid reached ~69 Å square. Then I stop. then again include the small molecule to final system_shrink.gro file and after that I perform the steps that is given in tutorial. is this the right way. I am doing this because we have to show the interaction of ligand and protein. I first created the ligand protein complex and at the time of running inflategro.pl command I separate the ligand molecule and again include it after iterations of scaling down by 0.95. rest of the steps is same as given in tutorial. one more query can we use orientation of protein in membrane database http://opm.phar.umich.edu/ for orientation of protein instead of editconf??? as it is not giving me the correct alignment. please help. >On 8/11/14, 3:33 AM, neha bharti wrote: > >Hello All > > > >I am trying to perform MD for protein-ligand complex in POPC with charmm36 > >force field and also follow Justin A. Lemkul tutorial using Gromacs VERSION > >4.5.5. > > > >As I am working on Protein-Ligand complex I am having few queries: > > > >1) The .pdb file was oriented along the z-axis using editconf -princ, > >followed by a rotation. We have to perform this step before separating the > >protein and ligand from the pdb file so that ligand also rotated along the > >same axis?? > > > > > >2) For orientation I use the following command. > > > >editconf -princ -f protein.pdb -o prot
[gmx-users] Problem in Ligand-Protein complex in POPC
Hello All I am trying to perform MD for protein-ligand complex in POPC with charmm36 force field and also follow Justin A. Lemkul tutorial using Gromacs VERSION 4.5.5. As I am working on Protein-Ligand complex I am having few queries: 1) The .pdb file was oriented along the z-axis using editconf -princ, followed by a rotation. We have to perform this step before separating the protein and ligand from the pdb file so that ligand also rotated along the same axis?? 2) For orientation I use the following command. editconf -princ -f protein.pdb -o protein_princ.pdb editconf -rotate 0 0 90 -f protein_princ.pdb -o protein_princ_rotate.pdb But when I include the POPC then saw that The protein is parallel align with popc which is not correct. I also use editconf -rotate 0 90 0 -f protein_princ.pdb -o protein_princ_rotate.pdb but still the alignment is same. Should I use only editconf -princ command and skip the rotation part or what else I can do?? 3) As* InflateGRO* script can not deal with ligand. So when should I include my ligand file in protein?? I have included it before system creation and at the time of using *InflateGRO* script I remove my ligand file and again insert it after perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat before solvating the system with water. Is this the right way or I have to do it by another way?? Please Help. With Regards Neha Bharty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Positive potential energy during Energy minimization step
I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. After Adding Ion genion -s ions.tpr -o pro_POPC_sol_ions.gro -p topol.top -pname NA -np 1 -nname CL I preform energy minimization step. In energy minimization step I am getting possitive potential enargy: Steepest Descents converged to machine precision in 18 steps, but did not reach the requested Fmax < 1000. Potential Energy = 6.1499341e+17 Maximum force =inf on atom 3300 Norm of force = 5.4206209e+18 its mention in the tutorial verify that the values of Epot and Fmax are reasonable before continuing I am trying alot but not able to fix the issue. Its mention in tutorial but I am not able to find the exactly what to do. please help. With Regards Neha bharty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] can we use Area per lipid: 1.00 nm^2
Hello All I am trying to perform MD for protein-ligand complex in popc lipid with Charmm36 force field and also follow Justin A. Lemkul tutorial. I performed perl inflategro.pl system.gro 4 POPC 0 system_inflated.pdb 5 area.dat followed by energy minimization then, perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat followed by energy minimization then after 16 iteration of scaling down by 0.95 I got Area per lipid: 1.00 nm^2. In 17th iteration Area per lipid become 0.80 nm^2. but after that when I visualize the .gro file i.e system_shrink17.gro the ligand molecule is far from protein and out of lipid. But till 16th iteration its inside the lipid in its normal position. Should I perform till 16th iteration which gives area per lipid 1.00 nm^2 ? Is it a good value for Area per lipid ?? or there is some error in my files. My topology file is : ; Include forcefield parameters #include "charmm36_lipid.ff/forcefield.itp" ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include ligand topology #include "LIG.itp" ; Ligand position restraints #ifdef POSRES #include "posre_LIG.itp" #endif [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] . . . . . . ; Strong position restraints for InflateGRO #ifdef POSRES_STRONG #include "strong_posre.itp" #endif ; Include POPC chain topology #include "popc.itp" ; Include water topology #include "charmm36_lipid.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "charmm36_lipid.ff/ions.itp" [ system ] ; Name Gyas ROwers Mature At Cryogenic Speed [ molecules ] ; Compound#mols Protein 1 LIG 1 POPC 128 Please Help Thank you very much. With Regards Neha bharty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error in Ligand position restraints
Hello All I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I successfully performed till perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat After this when I started performing energy minimization part it gives error : Fatal error: [ file strong_posre.itp, line 6979 ]: Atom index (6975) in position_restraints out of bounds (1-6974). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. I think the problem is that I have included position restraints for protein in topology file but not includes position restraints for ligand in that file. when I added ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include "strong_posre.itp" #endif to my topology file it consider both protein and ligand so the number of residue present in my position restraint file and Strong position restraint is different. I also check it by adding position restraint for ligand in my topology file. but it still giving the same error. I also check by merging position restraint file for ligand and protein but the same error is present. This is my topology file: ; Include forcefield parameters #include "charmm36_lipid.ff/forcefield.itp" ; Include ligand topology #include "lig.itp" [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ... ... ... ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Ligand position restraints #ifdef POSRES #include "posre_lig.itp" #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include "strong_posre.itp" #endif ; Include POPC chain topology #include "popc.itp" ; Include water topology #include "charmm36_lipid.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "charmm36_lipid.ff/ions.itp" [ system ] ; Name Gyas ROwers Mature At Cryogenic Speed [ molecules ] ; Compound#mols Protein 1 lig 1 POPC128 I have also check by changing the position of lig.itp file and posre_lig file by keeping them together like ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include ligand topology #include "lig.itp" ; Ligand position restraints #ifdef POSRES #include "posre_lig.itp" #endif then it gives another error because of the change in position of ligand topology file. Fatal error: Syntax error - File cyc.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Please Help. Thanks in Advance With Regards Neha bharty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error while running InflateGRO File
Hello All I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I generated small molecule topology file from SwissParam which provides .pdb file for ligand molecule. I don't have .gro file for small molecule thats why I have created all the file in .pdb file format. when I run: perl inflategro.pl system.pdb 4 POPC 0 system_inflated.gro 5 area.dat it gives error : Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... How to work with .pdb file to run inflategro.pl command?? can anyone please help me out how to solve this error. Thanks in advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Error in inflategro.pl
Hello All I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I generated small molecule topology file from SwissParam which provides .pdb file for ligand molecule. I don't have .gro file for small molecule thats why I have created all the file in .pdb file format. when I run: perl inflategro.pl system.pdb 4 POPC 0 system_inflated.gro 5 area.dat it gives error : Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... How to work with .pdb file to run inflategro.pl command?? can anyone please help me out how to solve this error. Thanks in advance Neha bharti -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem in Molecular dynamics of ligand protein complex in POPC lipid
Hello All I an trying molecular dynamics simulation of ligand protein complex in popc lipid with charmm36 force field and also follow Justin tutorial. But in that tutorial its only for protein not for ligand protein complex. I also took help of Justin protein-ligand complex tutorial. But while performing energy minimization step in "Pack the lipids around the protein " its giving following error: Fatal error: Syntax error - File cyc.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes my topology file is : ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include "strong_posre.itp" #endif ; Include ligand topology #include "cyc.itp" ; Ligand position restraints #ifdef POSRES #include "posre_cyc.itp" #endif ; Include POPC chain topology #include "popc.itp" ; Include water topology #include "charmm36.ff_lipid/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "charmm36.ff_lipid/ions.itp" [ system ] ; Name Protein in Lipid [ molecules ] ; Compound#mols Protein 1 LIG1 POPC128 I also check my changing the position of LIG and POPC like POPC128 LIG 1 But it still giving the same error.. Can any one please help me out for this.. Is there any tutorial for ligand protein complex in lipid??? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
