[gmx-users] Energy minimization issue
Dear Gromacs users, I'm simulation a double chain protein-ligand complex using Amber force field. I have written parameters and generated the topology. The energy minimization of the complex gives me the following error: *Energy minimization has stopped, but the forces have not converged to the* *requested precision Fmax < 1000 (which may not be possible for your system).* *It stopped because the algorithm tried to make a new step whose size was too* *small, or there was no change in the energy since last step. Either way, we* *regard the minimization as converged to within the available machine* *precision, given your starting configuration and EM parameters* *Double precision normally gives you higher accuracy, but this is often not* *needed for preparing to run molecular dynamics.* *You might need to increase your constraint accuracy, or turn* *off constraints altogether (set constraints = none in mdp file)* Could you please tell me what is the issue and provide some suggestions Thank you *Best regards* *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics -- 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] Add missing residues
Hello everyone, Can someone post the best tool available for building missing residues in the crystal structure? I need the complete structure (2 missing residues) for carrying out simulation studies. Thank you *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics -- 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] Invalid order for directive X
Hi Mark, Thank you for your quick reply. You mean by 'the acpype files must be edited to have all the atom types in a block before any of the molecules' all the files with GMX as I have used amberff99sb. There are many files for charmm, opls, ... In my case, I should see the following files: ACT_GMX.gro. ACT_GMX.itp, ACT_NEW.pdb ? Khadija *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics -- 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] Invalid order for directive X
Hello, I have read the documentation and tried to solve the problem but still having the same error. Any suggestions, please? *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics -- 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] Invalid order for directive X
3.34720 1 ; O1-C1- C2-H2 2 1 4 6 9 180.00 0.33472 3 ; O1-C1- C2-H2 2 1 4 7 9 0.00 0.0 0 ; O1-C1- C2-H3 2 1 4 7 9 0.00 3.34720 1 ; O1-C1- C2-H3 2 1 4 7 9 180.00 0.33472 3 ; O1-C1- C2-H3 2 1 4 8 9 0.00 0.0 0 ; O1-C1- C2-H4 2 1 4 8 9 0.00 3.34720 1 ; O1-C1- C2-H4 2 1 4 8 9 180.00 0.33472 3 ; O1-C1- C2-H4 3 1 4 6 9 180.00 0.0 2 ; O2-C1- C2-H2 3 1 4 7 9 180.00 0.0 2 ; O2-C1- C2-H3 3 1 4 8 9 180.00 0.0 2 ; O2-C1- C2-H4 4 1 3 5 9 180.00 9.62320 2 ; C2-C1- O2-H1 [ dihedrals ] ; impropers ; treated as propers in GROMACS to use correct AMBER analytical function ;i j k l func phase kd pn 3 1 2 4 4 180.00 4.60240 2 ; O2-C1- O1-C2 Is it a mistake in the directives order in .itp and .top? Can someone give me a suggestion to fix the issue Thank you *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics -- 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 and ion topology
Can anyone help, please? *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics Phone: 9584 On Tue, Jul 4, 2017 at 12:33 PM, Khadija Amine <kh.ami...@gmail.com> wrote: > Dear gromacs users, > > I have a protein with GNP ligand and acetate ACT ion that I want to > simulate. > > I have prepared topologies for both GNP and ACT with PRODRG program. > > My first question is: Where should I exactly include the ACT.itp and > GNP.itp into topol.top file? > > My second question is: > I have Copied and pasted the coordinates from my two molecules files onto > the end of the protein.gro file. I have changed the number at the top or > beginning of the file from as it should be to corrected the total number of > atoms in the file. > > Should I change the atom number column and renumber the atoms with the new > ones? > > Is this will affect the position of the ligand and the ions in the protein > structure? > > Thank you > > *Khadija Amine* > Ph.D. Biology and Health > Biochemistry & Bioinformatics > Phone: 9584 > -- 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 and ion topology
Dear gromacs users, I have a protein with GNP ligand and acetate ACT ion that I want to simulate. I have prepared topologies for both GNP and ACT with PRODRG program. My first question is: Where should I exactly include the ACT.itp and GNP.itp into topol.top file? My second question is: I have Copied and pasted the coordinates from my two molecules files onto the end of the protein.gro file. I have changed the number at the top or beginning of the file from as it should be to corrected the total number of atoms in the file. Should I change the atom number column and renumber the atoms with the new ones? Is this will affect the position of the ligand and the ions in the protein structure? Thank you *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics Phone: 9584 -- 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] Issue with the PDB generated after topology
Thank you, Mark. I understand from your suggestion, that what I got from topology and solvation phases is correct, and MD simulations even if it affects the numbering of the structure but the simulation results remain unaffected and I could renumber my residues at the end of simulation as it should be. This the first time I'm facing this case as it's the first time I'm running MD simulation of a protein complex. Khadija *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics Phone: 9584 -- 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] Issue with the PDB generated after topology
Hi, I have already converted the .gro file to .pdb file and I'm not able to see the two separated chains. Khadija *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics Phone: 9584 -- 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] Issue with the PDB generated after topology
Hi Mark, Is there any way to renumber my protein sequence at the end of the simulation? The numbering is very important in RMSF plot for example. Thank you *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics Phone: 9584 -- 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] Issue with the PDB generated after topology
Dear Mark, Thank you for your reply. My starting pdb sequence on pymol is: A 1-166, B 54-131 After topology generation and solvation, I can display the whole structure with the two chains A and B but in terms of sequence, the chain B is absent. Please, let me know if any further information needed. Khadija *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics Phone: 9584 -- 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] Issue with the PDB generated after topology
Dear Gromacs users, I'm running a protein complex simulations with the gromacs software. My complex is two different proteins named chain A (1-166 aa) and chain B (55-131)with 3 ions and one ligand. I have produced the topology for the every component of my complex using pdb2gmx program. However, when I have visualised the resulted pdb file with pymol, I can see the two displayed proteins but the amino acids sequence is not complete. I can see the chain A and not the chain B. Please, how can I fix this issue? Khadija *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics Phone: 9584 -- 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] Hbonds analysis
Thank you Dario and Amir for your help. I'll try with .gro file as suggested. Khadija *Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* On Sun, Dec 11, 2016 at 11:39 AM, Khadija Amine <kh.ami...@gmail.com> wrote: > Dear Gromacs users, > > I'm simulating a system of protein-protein complex. > One of the interesting analysis I would like to perform is to compute H > bonds between two important residues. > > I want to plot a graph of one specific residue located in the first > protein (chain A) that make hydrogen bond interactions with another > interface residue in the second protein (chain B). I just want to analyze > how many times residue 1 make or lose the interactions with residue 2 > during the whole simulation (time frame : 20ns) . > > If someone can help me make index for the residue 1 in the chain A and > residue 2 in the chain B. > > Thank you > > *Khadija AMINE* > > > *Computational Biology* > *Postdoctoral Research Associate* > *Carnegie Mellon University* > -- 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] Hbonds analysis
Dear Gromacs users, I'm simulating a system of protein-protein complex. One of the interesting analysis I would like to perform is to compute H bonds between two important residues. I want to plot a graph of one specific residue located in the first protein (chain A) that make hydrogen bond interactions with another interface residue in the second protein (chain B). I just want to analyze how many times residue 1 make or lose the interactions with residue 2 during the whole simulation (time frame : 20ns) . If someone can help me make index for the residue 1 in the chain A and residue 2 in the chain B. Thank you *Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* -- 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] Free energy calculation
Could you please propound a suggestion more helpful for doing it? Should I perform more MD simulation for my complexes? *Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* On Mon, Nov 28, 2016 at 4:56 PM, Khadija Amine <kh.ami...@gmail.com> wrote: > As I have mentioned in my first email, I want to calculate the free energy > of my protein-protein complex. > > I want to compute free energies for wild type and mutant complex and > compare them. > > *Khadija AMINE* > > > *Computational Biology* > *Postdoctoral Research Associate* > *Carnegie Mellon University* > > On Mon, Nov 28, 2016 at 4:02 PM, Khadija Amine <kh.ami...@gmail.com> > wrote: > >> Thank you Williams. >> >> I should try the umbrella sampling tutorial? >> >> My complex is simulated during 20ns. The starting files for free energy >> computing should be the MD production files? >> >> >> >> *Khadija AMINE* >> >> >> *Computational Biology* >> *Postdoctoral Research Associate* >> *Carnegie Mellon University* >> >> On Mon, Nov 28, 2016 at 12:56 PM, Khadija Amine <kh.ami...@gmail.com> >> wrote: >> >>> Dear Gromacs users, >>> >>> I have a system of protein-protein interaction. >>> >>> Is it possible to calculate the free energy of the complex? >>> >>> If it so, could you please give me an efficient tool to compute the free >>> energy calculation. >>> >>> Any suggestion. Thank you >>> >>> >>> *Khadija AMINE* >>> >>> >>> *Computational Biology* >>> *Postdoctoral Research Associate* >>> *Carnegie Mellon University* >>> >> >> > -- 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] Free energy calculation
As I have mentioned in my first email, I want to calculate the free energy of my protein-protein complex. I want to compute free energies for wild type and mutant complex and compare them. *Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* On Mon, Nov 28, 2016 at 4:02 PM, Khadija Amine <kh.ami...@gmail.com> wrote: > Thank you Williams. > > I should try the umbrella sampling tutorial? > > My complex is simulated during 20ns. The starting files for free energy > computing should be the MD production files? > > > > *Khadija AMINE* > > > *Computational Biology* > *Postdoctoral Research Associate* > *Carnegie Mellon University* > > On Mon, Nov 28, 2016 at 12:56 PM, Khadija Amine <kh.ami...@gmail.com> > wrote: > >> Dear Gromacs users, >> >> I have a system of protein-protein interaction. >> >> Is it possible to calculate the free energy of the complex? >> >> If it so, could you please give me an efficient tool to compute the free >> energy calculation. >> >> Any suggestion. Thank you >> >> >> *Khadija AMINE* >> >> >> *Computational Biology* >> *Postdoctoral Research Associate* >> *Carnegie Mellon University* >> > > -- 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] Free energy calculation
Thank you Williams. I should try the umbrella sampling tutorial? My complex is simulated during 20ns. The starting files for free energy computing should be the MD production files? *Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* On Mon, Nov 28, 2016 at 12:56 PM, Khadija Amine <kh.ami...@gmail.com> wrote: > Dear Gromacs users, > > I have a system of protein-protein interaction. > > Is it possible to calculate the free energy of the complex? > > If it so, could you please give me an efficient tool to compute the free > energy calculation. > > Any suggestion. Thank you > > > *Khadija AMINE* > > > *Computational Biology* > *Postdoctoral Research Associate* > *Carnegie Mellon University* > -- 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] Free energy calculation
Dear Gromacs users, I have a system of protein-protein interaction. Is it possible to calculate the free energy of the complex? If it so, could you please give me an efficient tool to compute the free energy calculation. Any suggestion. Thank you *Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* -- 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] MD simulations of two chains protein
*Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* On Wed, Nov 16, 2016 at 9:15 AM, Khadija Amine <kh.ami...@gmail.com> wrote: > Hi Mark, > > Below, the link to the rmsf plot I had for my protein throughout 20 ns > simulation. > > https://www.dropbox.com/s/v67u8iplcyl506q/rmsfmergemut.png?dl=0 > > The command I used is: gmx rmsf -s XXX.tpr -f XXX.xtc -o rmsf.xvg -oq > rmsf.pdb -res > > Thank you > > *Khadija AMINE* > > > *Computational Biology* > *Postdoctoral Research Associate* > *Carnegie Mellon University* > > On Tue, Nov 15, 2016 at 10:50 AM, Khadija Amine <kh.ami...@gmail.com> > wrote: > >> Ok I will try that. >> >> There is a way to specify the regions to plot in RMSF using rms tool? >> >> Thank you >> >> *Khadija AMINE* >> >> >> *Computational Biology* >> *Postdoctoral Research Associate* >> *Carnegie Mellon University* >> >> On Tue, Nov 15, 2016 at 10:40 AM, Khadija Amine <kh.ami...@gmail.com> >> wrote: >> >>> Hello, >>> >>> Can someone show me how can I proceed? >>> >>> Thank you >>> >>> *Khadija AMINE* >>> >>> >>> *Computational Biology* >>> *Postdoctoral Research Associate* >>> *Carnegie Mellon University* >>> >>> On Mon, Nov 14, 2016 at 2:33 PM, Khadija Amine <kh.ami...@gmail.com> >>> wrote: >>> >>>> Dear Gromacs users, >>>> >>>> I need your help regarding MD simulation of two chains protein. >>>> The chain A is 2-78 aa, and the chain B is 1-168 aa. >>>> >>>> I started with the pdb file where there is specified names of the two >>>> chains as A and B. >>>> >>>> I did solvation of my system in a cubic box, I tried to open the >>>> pdb file issued from this step I didn't find the column specifying the >>>> chain names. >>>> >>>> I run 20 ns of MD for this protein. The RMSF plot of the protein seems >>>> to be overlapping from 1 to 78 and the rest of the residues flctuation >>>> is good. >>>> >>>> As it is the first time am facing such issues with protein with two >>>> chains, how can I avoid such overlap in RMSF plot? >>>> >>>> Is this linked to the chains numbering issued after writing the >>>> topology. >>>> >>>> Thank you >>>> >>>> *Khadija AMINE* >>>> >>>> >>>> *Computational Biology* >>>> *Postdoctoral Research Associate* >>>> *Carnegie Mellon University* >>>> >>> >>> >> > -- 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] MD simulations of two chains protein
Hi Mark, Below, the link to the rmsf plot I had for my protein throughout 20 ns simulation. https://www.dropbox.com/s/v67u8iplcyl506q/rmsfmergemut.png?dl=0 The command I used is: gmx rmsf -s XXX.tpr -f XXX.xtc -o rmsf.xvg -oq rmsf.pdb -res Thank you *Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* On Tue, Nov 15, 2016 at 10:50 AM, Khadija Amine <kh.ami...@gmail.com> wrote: > Ok I will try that. > > There is a way to specify the regions to plot in RMSF using rms tool? > > Thank you > > *Khadija AMINE* > > > *Computational Biology* > *Postdoctoral Research Associate* > *Carnegie Mellon University* > > On Tue, Nov 15, 2016 at 10:40 AM, Khadija Amine <kh.ami...@gmail.com> > wrote: > >> Hello, >> >> Can someone show me how can I proceed? >> >> Thank you >> >> *Khadija AMINE* >> >> >> *Computational Biology* >> *Postdoctoral Research Associate* >> *Carnegie Mellon University* >> >> On Mon, Nov 14, 2016 at 2:33 PM, Khadija Amine <kh.ami...@gmail.com> >> wrote: >> >>> Dear Gromacs users, >>> >>> I need your help regarding MD simulation of two chains protein. >>> The chain A is 2-78 aa, and the chain B is 1-168 aa. >>> >>> I started with the pdb file where there is specified names of the two >>> chains as A and B. >>> >>> I did solvation of my system in a cubic box, I tried to open the >>> pdb file issued from this step I didn't find the column specifying the >>> chain names. >>> >>> I run 20 ns of MD for this protein. The RMSF plot of the protein seems >>> to be overlapping from 1 to 78 and the rest of the residues flctuation >>> is good. >>> >>> As it is the first time am facing such issues with protein with two >>> chains, how can I avoid such overlap in RMSF plot? >>> >>> Is this linked to the chains numbering issued after writing the topology. >>> >>> Thank you >>> >>> *Khadija AMINE* >>> >>> >>> *Computational Biology* >>> *Postdoctoral Research Associate* >>> *Carnegie Mellon University* >>> >> >> > -- 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] MD simulations of two chains protein
Hello, Can someone show me how can I proceed? Thank you *Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* On Mon, Nov 14, 2016 at 2:33 PM, Khadija Amine <kh.ami...@gmail.com> wrote: > Dear Gromacs users, > > I need your help regarding MD simulation of two chains protein. > The chain A is 2-78 aa, and the chain B is 1-168 aa. > > I started with the pdb file where there is specified names of the two > chains as A and B. > > I did solvation of my system in a cubic box, I tried to open the pdb file > issued from this step I didn't find the column specifying the chain names. > > I run 20 ns of MD for this protein. The RMSF plot of the protein seems to > be overlapping from 1 to 78 and the rest of the residues flctuation is > good. > > As it is the first time am facing such issues with protein with two > chains, how can I avoid such overlap in RMSF plot? > > Is this linked to the chains numbering issued after writing the topology. > > Thank you > > *Khadija AMINE* > > > *Computational Biology* > *Postdoctoral Research Associate* > *Carnegie Mellon University* > -- 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] MD simulations of two chains protein
Dear Gromacs users, I need your help regarding MD simulation of two chains protein. The chain A is 2-78 aa, and the chain B is 1-168 aa. I started with the pdb file where there is specified names of the two chains as A and B. I did solvation of my system in a cubic box, I tried to open the pdb file issued from this step I didn't find the column specifying the chain names. I run 20 ns of MD for this protein. The RMSF plot of the protein seems to be overlapping from 1 to 78 and the rest of the residues flctuation is good. As it is the first time am facing such issues with protein with two chains, how can I avoid such overlap in RMSF plot? Is this linked to the chains numbering issued after writing the topology. Thank you *Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* -- 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] Molecular dynamic simulations of Protein-DNA complex
Hello Erik, Thank you. I mean that the global shape of the complex is lost from 5ns to 10ns. After that, the structural flexibility of the complex is regained. *Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* On Mon, Oct 24, 2016 at 11:06 AM, Khadija Amine <kh.ami...@gmail.com> wrote: > Dear Gromacs users, > > I have run 20ns of MD simulations of my protein-DNA complex. > > All my trajectory files have been combined in a same final file. > > I have visualized that trajectory file using pymol software. > Unfortunately, the DNA structure and some parts of the complexed protein > structure show deformations. > > How can I prevent this issue and obtain correct structure, movement of my > complex? > > This is the first time I perform MD for the protein - DNA complex. > > Thank you > > *Khadija AMINE* > > > *Computational Biology* > *Postdoctoral Research Associate* > *Carnegie Mellon University* > -- 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] Molecular dynamic simulations of Protein-DNA complex
Dear Gromacs users, I have run 20ns of MD simulations of my protein-DNA complex. All my trajectory files have been combined in a same final file. I have visualized that trajectory file using pymol software. Unfortunately, the DNA structure and some parts of the complexed protein structure show deformations. How can I prevent this issue and obtain correct structure, movement of my complex? This is the first time I perform MD for the protein - DNA complex. Thank you *Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* -- 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.
