[gmx-users] Pulling along dihedral angle as the reaction coordinate
I came across one such application name PLUMED plugin for gromacs, for dihedral restraints as the reaction coordinate. If you can suggest any other application for the same, kindly let me know. --Thanks Neeru > On 4/15/13 2:27 AM, neeru sharma wrote: > > Dear gromacs users, > > > > > > I want to calculate PMF using pull code in gromacs, taking a psi angle as > > the reaction coordinate. > > I have a doubt where it is possible with the geometry options, currently > > available in gromacs? > > > > This is an application of either dihedral restraints or the new enforced > rotation options. > > -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] Pulling along dihedral angle as the reaction coordinate
Dear gromacs users, I want to calculate PMF using pull code in gromacs, taking a psi angle as the reaction coordinate. I have a doubt where it is possible with the geometry options, currently available in gromacs? Thanks and regards Neeru -- 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] Restraining water molecule
> > Message: 1 > Date: Thu, 21 Mar 2013 07:05:44 -0400 > From: Justin Lemkul > Subject: Re: [gmx-users] Restraining water molecule > To: Discussion list for GROMACS users > Message-ID: <514ae988.4050...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 3/21/13 4:29 AM, neeru sharma wrote: > >> Message: 6 > >> Date: Wed, 20 Mar 2013 09:04:05 -0400 > >> From: Justin Lemkul > >> Subject: Re: [gmx-users] Restraining water molecule > >> To: Discussion list for GROMACS users > >> Message-ID: > >> < > >> caduqwc5+fotchpmi0pqeexcnpkbtqa-yb0px1p889gy3jza...@mail.gmail.com> > >> Content-Type: text/plain; charset=ISO-8859-1 > >> > >> On Wed, Mar 20, 2013 at 8:57 AM, neeru sharma >>> wrote: > >> > >>> Dear gromacs users, > >>> > >>> I am simulating a system of Protein-ion-GTP with One Water molecule. I > >> want > >>> to restrain this system (along with this water molecule) for > minimization > >>> and equilibration. > >>> > >>> Everytime I run this by specifying the .itp files, it gives the error > of > >>> misplacement as follows: > >>> > >>> *"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." > >>> * > >>> > >>> The sequence I am giving in the topology file is like this: > >>> > >>> > >>> > >>> * > >>> ; Include Position restraint file for Protein-ion-GTP-Water > >>> #ifdef POSRES_LIGAND > >>> #include "posre_comp.itp" > >>> #endif > >>> > >>> ; Include ligand topology > >>> #include "gtp.itp" > >>> > >>> ; Include water topology > >>> #include "gromos43a1.ff/spc.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 "gromos43a1.ff/ions.itp"* > >>> * > >>> > >>> [ system ] > >>> ; Name > >>> Protein in water > >>> > >>> [ molecules ] > >>> ; Compound#mols > >>> Protein 1 > >>> GTP 1 > >>> SOL 1 > >>> SOL 12179 > >>> NA 8 > >>> * > >>> > >>> Can anybody help me figuring out the issue,where I am doing wrong? Any > >>> suggestion is welcome > >>> > >>> > >> If you want to restrain a single water molecule, it needs to be defined > as > >> its own [moleculetype] or as a part of the protein [moleculetype]. > Breaking > >> apart a continuous block of water causes problems with the SETTLE > >> algorithm, so you will need to manually specify three constraints > (OW-HW1, > >> OW-HW2, and HW1-HW2) for this water molecule, while the remaining bath > of > >> solvent would be handled by SETTLE. > >> > >> -Justin > >> > >> -- > >> > >> > >> > >> Justin A. Lemkul, Ph.D. > >> Research Scientist > >> Department of Biochemistry > >> Virginia Tech > >> Blacksburg, VA > >> jalemkul[at]vt.edu | (540) > >> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >> > >> > >> > >> > >> -- > >> > >> -- > >> gmx-users mailing list > >> gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> > >> End of gmx-users Digest, Vol 107, Issue 81 > >> ** > >> > > > > I tried restraining the
[gmx-users] Re: gmx-users Digest, Vol 107, Issue 81
> Message: 6 > Date: Wed, 20 Mar 2013 09:04:05 -0400 > From: Justin Lemkul > Subject: Re: [gmx-users] Restraining water molecule > To: Discussion list for GROMACS users > Message-ID: > < > caduqwc5+fotchpmi0pqeexcnpkbtqa-yb0px1p889gy3jza...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Wed, Mar 20, 2013 at 8:57 AM, neeru sharma >wrote: > > > Dear gromacs users, > > > > I am simulating a system of Protein-ion-GTP with One Water molecule. I > want > > to restrain this system (along with this water molecule) for minimization > > and equilibration. > > > > Everytime I run this by specifying the .itp files, it gives the error of > > misplacement as follows: > > > > *"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." > > * > > > > The sequence I am giving in the topology file is like this: > > > > > > > > * > > ; Include Position restraint file for Protein-ion-GTP-Water > > #ifdef POSRES_LIGAND > > #include "posre_comp.itp" > > #endif > > > > ; Include ligand topology > > #include "gtp.itp" > > > > ; Include water topology > > #include "gromos43a1.ff/spc.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 "gromos43a1.ff/ions.itp"* > > * > > > > [ system ] > > ; Name > > Protein in water > > > > [ molecules ] > > ; Compound#mols > > Protein 1 > > GTP 1 > > SOL 1 > > SOL 12179 > > NA 8 > > * > > > > Can anybody help me figuring out the issue,where I am doing wrong? Any > > suggestion is welcome > > > > > If you want to restrain a single water molecule, it needs to be defined as > its own [moleculetype] or as a part of the protein [moleculetype]. Breaking > apart a continuous block of water causes problems with the SETTLE > algorithm, so you will need to manually specify three constraints (OW-HW1, > OW-HW2, and HW1-HW2) for this water molecule, while the remaining bath of > solvent would be handled by SETTLE. > > -Justin > > -- > > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > -- > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 107, Issue 81 > ** > I tried restraining the single water molecule by specifying the Protein-Ion-GTP-Water as one index group. The itp file, I used for this water molecule was as follows: *[ moleculetype ] ; molname nrexcl WAT 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass #ifndef HEAVY_H 1 O 1WAT O 1 -0.82 15.99940 2 H 1WAT H1 1 0.411.00800 3 H 1WAT H2 1 0.411.00800 #else 1 O 1WAT O 1 -0.829.95140 2 H 1WAT H1 1 0.414.03200 3 H 1WAT H2 1 0.414.03200 #endif #ifndef FLEXIBLE [ settles ] ; O funct doh dhh 1 1 0.1 0.16330 [ exclusions ] 1 2 3 2 1 3 3 1 2 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 0.1 345000 1 3 1 0.1 345000 0.1 345000 [ angles ] ; i j k funct angle force.c. 2 1 3 1 109.47 383 109.47 383 #endif* But, ended with the fatal error: *Fatal error: The [molecules] section of your topology specifies more than one block of a [moleculetype] with a [settles] block. Only one such is allowed. If you are trying to pa
[gmx-users] Restraining water molecule
Dear gromacs users, I am simulating a system of Protein-ion-GTP with One Water molecule. I want to restrain this system (along with this water molecule) for minimization and equilibration. Everytime I run this by specifying the .itp files, it gives the error of misplacement as follows: *"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." * The sequence I am giving in the topology file is like this: * ; Include Position restraint file for Protein-ion-GTP-Water #ifdef POSRES_LIGAND #include "posre_comp.itp" #endif ; Include ligand topology #include "gtp.itp" ; Include water topology #include "gromos43a1.ff/spc.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 "gromos43a1.ff/ions.itp"* * [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein 1 GTP 1 SOL 1 SOL 12179 NA 8 * Can anybody help me figuring out the issue,where I am doing wrong? Any suggestion is welcome --Thanks Neeru -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 106, Issue 62
> > On 2/12/13 1:12 AM, neeru sharma wrote: > > Dear Gromacs Users, > > > > > > I have simulated a system of protein-ion complex. As a part of the > > analysis, I want to see whether there are any H-bonds or other > interactions > > between the active site residues and the water surrounding those > residues. > > I was trying to perform the same using g_hbond program of gromacs, but > > could not get any output. I tried with varying the cut off value and as > > well specifying the "contact" option to look for the non H-bond > > interactions too, that fall within the cut off mentioned. > > > > Can anybody suggest me how to look for the H-bonds between protein > residues > > and water molecules? > > > > Your question and subject line refer to different things. Detecting > hydrogen > bonds between protein residues and water is trivial. Create index groups > for > the residues of interest and select these residues and water as the two > groups > for g_hbond. Water-mediated hydrogen bonds between residues, however, are > far > more difficult to obtain, but this topic has been covered many times in > the list > archive. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > - > Thanks Justin. It worked. Earlier I was trying just with the index file of the specific residues and without the index file for the specific water molecules. But now it works when I give the index file both for specific water and protein residues. --Neeru -- 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: Bins in wham analysis
Thanks Stephan for you suggestion. I will try the analysis with larger value of bins. --Neeru -- View this message in context: http://gromacs.5086.n6.nabble.com/Bins-in-wham-analysis-tp4999648p4999709.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Bins in wham analysis
Thanks Justin for your reply. I did see that the default bins value is 200, but I was not sure what does it signify. It says " no of bins used in the analysis". That's why I was confused whether it is equal to no. of umbrella sampling simulations we run and give input to g_wham. Thanks for clearing the doubt. --- Neeru -- View this message in context: http://gromacs.5086.n6.nabble.com/Bins-in-wham-analysis-tp4999648p4999707.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Bins in wham analysis
Dear Gromacs users, I have a query regarding the number of bins used in wham analysis. If I have performed by simulations over 15 umbrellas (15 different staring structures), what should be the ideal number of bins to perform wham analysis? Does it depend on the number of umbrellas. For example: 1) Should I use more than 15 bins in my case, and the one that gives proper overlap in histogram ? 2) Or any number of bins (even if it is less than 12) can be used, if I get proper overlap in my histogram output? Any suggestion is appreciated. -- Thanks and regards, Neeru Sharma -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Bins in wham analysis
Dear Gromacs users, I have a query regarding the number of bins used in wham analysis. If I have performed by simulations over 15 umbrellas (15 different staring structures), what should be the ideal number of bins to perform wham analysis? Does it depend on the number of umbrellas. For example: 1) Should I use more than 15 bins in my case, and the one that gives proper overlap in histogram ? 2) Or any number of bins (even if it is less than 12) can be used, if I get proper overlap in my histogram output? Any suggestion is appreciated. -- Thanks and regards, Neeru Sharma -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Final state not reached in pulling simulation
Thanks Justin for all your comments and suggestion. I am not using any position restraints as of now. But I will try out more parameters and more options. Thanks again. --Neeru -- View this message in context: http://gromacs.5086.n6.nabble.com/Final-state-not-reached-in-pulling-simulation-tp4999387p4999414.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Final state not reached in pulling simulation
Dear Justin, Thanks for the suggestion regarding the pull force. 1)I will try by reducing the pull force to 1000 and 100 KJmol/nm2 now. Regarding the force being applied in z-direction, after visualizing my trajectory i thought it would work by providing force in z-direction. 2)Regarding the protein rotation, it does not rotate over the time. There are just some localized changes in it. 3)Regarding the distance measurement, I am measuring the distance between the specific atoms of the residue and the atoms of the GTP. Till now, these distances as well as the overall protein geometry is maintained well in the range too. 4)If this kind of pulling does not work out in my case, I will again try it with using "position" geometry too with pull_vec1. Can you suggest why have I not reached the final distance at the end of the simulation? Is it because of the geometry that I have used, because the force constant is already too high in this case? Thanks again for your response. -- View this message in context: http://gromacs.5086.n6.nabble.com/Final-state-not-reached-in-pulling-simulation-tp4999387p4999399.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Final state not reached in pulling simulation
Dear Stephan, Actually I had less idea about the force parameters of the pulling simulation, that's why I started with this force. I will again retry by reducing the force to 1000 and 100 KJmol/nm-2 too. Any suggestion regarding the other parameters is also welcome!! Thanks for your response!! --Neeru -- View this message in context: http://gromacs.5086.n6.nabble.com/Final-state-not-reached-in-pulling-simulation-tp4999387p4999397.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Final state not reached in pulling simulation
Dear Thomas, Thanks for ur reply. I have visualized my trajectory and found no water molecule in between. Moreover, there are no residues in between the "Residue" and GTP molecule too. I feel I have already applied a large force for the pulling. Still I will consider you suggestion. One query regarding your suggestion. It one happens to find a water molecule in between the pulling groups, will removal of that water be a solution, because during the course of simulation it may happen that some other molecule again come between? Thanks anyways for you reply and suggestions. --Neeru -- View this message in context: http://gromacs.5086.n6.nabble.com/Final-state-not-reached-in-pulling-simulation-tp4999387p4999396.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Final state not reached in pulling simulation
Hello all, I m performing a pulling simulation on my Protein-Mg-GTP complex. I have considered pulling between the GTP and a residue of protein. The pull code in the .mdp file im using is as follows: ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups= 1 pull_group0 = GTP pull_group1 = Residue pull_rate1 = -0.5 ; 0.5 nm per ps = .05 nm per ns pull_k1 = 1 ; kJ mol^-1 nm^-2 The initial distance between GTP and the residue was 7 A and the desired one was 3A. After the completion of run (10ns), I could get a trajectory where the final distance was still 4.25 A. I tried to continue the simulation for another 10ns with the same value for pull_k1 parameter and one by increasing the value to 100,000 also. In both of the case, the trajectories showed the distance stabilized near _4.25 A only. Can anyone please tell me the reason behind it? What should I do, so that I could get the desired distance ? Any suggestion and help is welcome !!! Thanks, Neeru Sharma -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Final state not reached in pulling simulation
Hello all, I m performing a pulling simulation on my Protein-Mg-GTP complex. I have considered pulling between the GTP and a residue of protein. The pull code in the .mdp file im using is as follows: ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups= 1 pull_group0 = GTP pull_group1 = Residue pull_rate1 = -0.5 ; 0.5 nm per ps = .05 nm per ns pull_k1 = 1 ; kJ mol^-1 nm^-2 The initial distance between GTP and the residue was 7 A and the desired one was 3A. After the completion of run (10ns), I could get a trajectory where the final distance was still 4.25 A. I tried to continue the simulation for another 10ns with the same value for pull_k1 parameter and one by increasing the value to 100,000 also. In both of the case, the trajectories showed the distance stabilized near _4.25 A only. Can anyone please tell me the reason behind it? What should I do, so that I could get the desired distance ? Any suggestion and help is welcome !!! Thanks, Neeru Sharma -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Regarding parameters for pull_groups in mdp file for the pull code
Thanks Justin for your early response. I was confused about it, but now it's clear. Thanks --Neeru > Dear Gromacs Users, > > > I have some queries about the parameters in the .mdp file for the pull code. > > If I want to pull my ligand, towards specific atom/group of atoms from > the protein, how am I supposed to mentioned these in the mdp file? > > * > pull = umbrella > pull_geometry = distance > pull_start = yes > pull_ngroups= 1 > pull_group0 = Ligand > pull_group1 = Atom/group of atoms from the protein > * > > Here, I want to specify the pull_group0 as "Ligand" and pull_group1 as > "Atoms of the protein". My query is regarding these groups. Shall I > just write the name of the Ligand and Atoms (specifying the atom no) > or am I supposed to create a separate index file for each of them (one > for ligand and other for group of atoms) ? > All groups specified in the .mdp file must be either valid default groups or custom groups provided in an index file. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Regarding parameters for pull_groups in mdp file for the pull code
Dear Gromacs Users, I have some queries about the parameters in the .mdp file for the pull code. If I want to pull my ligand, towards specific atom/group of atoms from the protein, how am I supposed to mentioned these in the mdp file? * pull = umbrella pull_geometry = distance pull_start = yes pull_ngroups= 1 pull_group0 = Ligand pull_group1 = Atom/group of atoms from the protein * Here, I want to specify the pull_group0 as "Ligand" and pull_group1 as "Atoms of the protein". My query is regarding these groups. Shall I just write the name of the Ligand and Atoms (specifying the atom no) or am I supposed to create a separate index file for each of them (one for ligand and other for group of atoms) ? Any suggestion is welcome!! Thanks in advance. Neeru -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Re: Regarding umbrella sampling simulations along H-bonds
Dear Stephan Watkins, Thanks for your response. I would again like to specify my query to my main concerns. My main query lies for the 2 H-bonds: one between Protein and MG and other one between protein and GTP. 1) I have 2 configurations of my system. In the initial state: Prot-Mg-GTP complex (Without 2 hbonds ) and final state: Prot-Mg-GTP complex (With 2 hbonds ) I was looking, if there is some way to perform umbrella sampling and then perform WHAM analysis or to calculate PMF for this system, which would also be based these 2 Hbonds ? 2) Also, I have the trajectory traversing the formation of these Hbonds during the course of simulation. Can I use this trajectory to perform some analysis based on these H bonds in terms of free energy, PMF or energy barrier needed to reach to the final state? But as far as I understand, gromacs takes electrostatic energy term into consideration and there is no such specific treatment for H-bonds in terms of energy calculation. 3) One more thing, can I use pull code in my case where one atom (of the protein and connected to rest of the protein too) forms a H-bond with Mg and another atom with GTP ? 4) Or is there any better way to calculate some kind of energy barrier or PMF needed to form these 2 H-bonds along the simulation length? Any suggestion is welcome. Thanks, Neeru Dear Neeru Sharma, I know off hand from years of work with Mg-GTP sites, they are realativly rigid/staritforward. If the bonds arn't present with occupied GTP, or Mg at the beggining, you should equilabrate your starting structures more. Unless your looking at the GTP binding to Mg in which case, the Mg bonds should at least be present. Mg wont leave the site under norm conditions, unless the protein is unfolded (or recycled in cell biological or biochemical terms), or outcompeted with a higher affine ion. > Can anyone suggest me what parameters or pull_geometry shall I use, to > perform the same. Any suggestion is welcome! Thats too experiment specific to say, without knowing what your trying to look at. Grüess Stephan Watkins Original-Nachricht > Datum: Thu, 28 Jun 2012 23:30:38 +0530 > Von: neeru sharma > An: gmx-users@gromacs.org > Betreff: [gmx-users] Regarding umbrella sampling simulations along H-bonds > Dear Gromacs Users, > > I am simulating a system containing Protein-Mg-GTP complex. > > I intend to perform the umbrella sampling on the system to calculate > PMF and to perform wham analysis. > I have generated a series of conformations for the umbrella sampling. > My main consideration is towards the 2 H-bonds: one between Protein > and MG and other one between protein and GTP. Both of these bonds were > absent during the start of the simulation but formed when the > simulation was completed. > > Can anyone suggest me what parameters or pull_geometry shall I use, to > perform the same. Any suggestion is welcome! > > > -- > Thanks and regards, > Neeru -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Regarding umbrella sampling simulations along H-bonds
Dear Christopher Neale, Let me re-frame my question again. Though I am new to US, but I have a basic idea about performing US. My main query lies for these 2 H-bonds: one between Protein and MG and other one between protein and GTP. I want to know if I can perform umbrella sampling to explain the formation of these 2 H-bonds too, as I have to perform WHAM analysis too. My systems initial configuration: Prot-Mg-GTP complex (both the H bonds absent) Final configuration: Prot-Mg-GTP complex (both the H bonds present). I want to explain the formation of these bonds using US, but don't really know how to do it? Any suggestion is always welcome. Thanks and Regards, Neeru Dear Neeru: Please reformulate your question so that it is clear what you are asking. If your question is "how do I do US?" you are unlikely to get much help here beyond being directed to one of the US tutorials that you can find by a google search. If however, you know how to do US but have a particular question about some aspect of the formation of these H-bonds, then I'll note that I don't actually see any question on that topic in your post. -- original message -- Dear Gromacs Users, I am simulating a system containing Protein-Mg-GTP complex. I intend to perform the umbrella sampling on the system to calculate PMF and to perform wham analysis. I have generated a series of conformations for the umbrella sampling. My main consideration is towards the 2 H-bonds: one between Protein and MG and other one between protein and GTP. Both of these bonds were absent during the start of the simulation but formed when the simulation was completed. Can anyone suggest me what parameters or pull_geometry shall I use, to perform the same. Any suggestion is welcome! -- Thanks and regards, Neeru -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Regarding umbrella sampling simulations along H-bonds
Dear Gromacs Users, I am simulating a system containing Protein-Mg-GTP complex. I intend to perform the umbrella sampling on the system to calculate PMF and to perform wham analysis. I have generated a series of conformations for the umbrella sampling. My main consideration is towards the 2 H-bonds: one between Protein and MG and other one between protein and GTP. Both of these bonds were absent during the start of the simulation but formed when the simulation was completed. Can anyone suggest me what parameters or pull_geometry shall I use, to perform the same. Any suggestion is welcome! -- Thanks and regards, Neeru -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 98, Issue 44
> > Message: 1 > Date: Thu, 07 Jun 2012 08:53:22 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] Regarding Free Energy calculation tutorial > To: Discussion list for GROMACS users > Message-ID: <4fd0a442.6000...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 6/7/12 8:26 AM, neeru sharma wrote: > > Dear Justin, > > > > Greetings of the day!! > > > > I am following your tutorial for the calculation of free energy change > in gromacs. > > > > It says about the change in state A and state B. I have a query > regarding these > > states. What are the 2 states A and B in the tutorial and how can I > define these > > 2 states for my system? > > > > The changes applied between state A and B are defined in the .mdp file > based on > the couple-lambda0 and couple-lambda1 settings. These are used to > transform > either vdW or Coulombic interactions. If you need to make some other type > of > change (i.e. a mutation), then you would do so in the topology, setting > B-state > parameters explicitly. > > > For example, I have a Protein-Mg-GTP complex (In initial state A, 2 > specific > > H-bonds are absent and in the final state, these 2 H-bonds are present). > So, how > > can I implement this for the calculation of change in free energy to my > system? > > > > This doesn't sound like something that can be done with the decoupling > technique; it sounds to me more like a structural change. Perhaps you can > do > some careful calculations using the pull code, but it is not clear to me > what > you are trying to do. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > Thanks for the reply. Well,yes it is more of the strutural change in case of my case which can also be quantified in terms of presence and absence of these 2 H-bonds. And as the two structures are distinct from each other too, there has to be some energy change which I want to calculate too. Moreover, this structure change and the appearance of these H-bonds take long time and cross a energetic barrier too, I am trying to calculate this energy barrier too. Regarding the pull code, I will also try it for my system --- Neeru -- 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] Regarding Free Energy calculation tutorial
Dear Justin, Greetings of the day!! I am following your tutorial for the calculation of free energy change in gromacs. It says about the change in state A and state B. I have a query regarding these states. What are the 2 states A and B in the tutorial and how can I define these 2 states for my system? For example, I have a Protein-Mg-GTP complex (In initial state A, 2 specific H-bonds are absent and in the final state, these 2 H-bonds are present). So, how can I implement this for the calculation of change in free energy to my system? Thanks and Regards, Neeru Sharma CDAC, Pune, India -- 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] Regarding Free energy (Energy barrier) calculation
Dear Gromacs Users, Greetings of the day!! I am simulating a system of Protein-Mg-GTP complex. There are 2 states for the same, state 1 and state2. The difference lies in the presence of 2 specific H-bonds in the state 2 ,which are absent in state 1. Now, I need to find the energy barrier that was crossed to reach state 2 (2 H-bonds) from state 1. Can you suggest me some way to find this energy barrier in gromacs ? Thanks in anticipation. -- Regards, Neeru Sharma Project Engineer, Molecular Modelling Team, Bioinformatics Group, Centre for Development of Advanced Computing (CDAC), Ganeshkhind, Pune University Campus, Pune, Maharashtra - 411007 -- 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 in visualizing protein-ion complex trajectory in vmd
Dear gromacs users, I am running steered MD simulation using Plumed plugin in gromacs for a system consisting of Protein-Mg-GTP complex. I have to calculate the distance of specific atoms with Mg and GTP. While visualizing the trajectories using vmd, I am encountering some problems. 1) While using the "-pbc" flag with "whole" option, the protein is visualized properly, but the Mg and GTP are showing jumps moving away from the protein structure. That is why, the distance between Mg, GTP with atoms of the protein is not coming out properly. 2) While using the "-pbc" flag with "nojump" option, the protein is visible in stretched and distorted geometry, but the Mg and GTP are intact with the structure. Here, the distance between Mg,GTP with atoms of the protein is calculated correctly. 3) Then, I tried with both the whole and nojump options,used in succession (first whole and then nojump), but still the protein is not visualized properly. It is visible in stretched geometry only, as was visible with nojump. Can anyone help me regarding the problems I am facing with the visualization? Any help will be highly appreciated. Thanks in advance Regards, Neeru -- 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] PLUMED plugin in gromacs for protein system
Dear gromacs users, I am a gromacs user and need some help regarding the implementation of PLUMED plugin in gromacs. I am simulating a system containing Protein-Mg-GDP and Protein-Mg-GTP using Gromacs which is a 166 residue protein+mg+GTP/GDP complex. I have already carried out classical MD simulation for the Protein-Mg-GDP complex. Then, I replaced GDP with GTP in the complex and now have to analyse the structural changes in the Protein-Mg-GTP complex during the simulation. I tried to perform classical MD simulation for the Protein-Mg-GTP complex too. But, as GDP to GTP state transition is a millisecond time-scale event, through classical MD, it seems practically impossible to achieve this time-scale transition. I was looking for the methods available in gromacs that can accelerate this event. I came across the PLUMED plugin. I have some queries with respect to the above matter. 1) Can we manually specify simulation length when performing the simulation, that we want to finish the simulation in the given specified time duration? 2) How can we specify reaction coordinates (Eg: The RMSD with the desired output state, Specific H-bonding or distance pattern etc) for the simulation, as I already have the crystal structure available with me for the Protein-Mg-GTP complex (output state desired to be achieved with the simulation). As, I am new to gromacs, can you please help me regarding the above mentioned matter, usage of plumed plugin for protein system and how it can be approached with my system? Any help will be highly appreciated. Thanks in advance Regards, Neeru -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 96, Issue 146
Hi Matthew, Thanks for your response. I will definitely look into the NEB method, suggested by you. By the way, do you have any idea about Flooding approach or the PLUMED plugin in gromacs for performing such simulations? Thanks in advance. Neeru. > Hi Neeru, > > Any number of enhanced sampling techniques might do this, but weighted > ensemble, forward flux sampling, milestoning, and transition path > sampling (all described in (Zwier, M. C.; Chong, L. T. Current Opinion > in Pharmacology 2010, 10, 745–752.) and the nudged elastic band method > (Bergonzo, C., Campbell, A.J., Walker, R.C., Simmerling, C., "A > Partial Nudged Elastic Band Implementation for Use with Large or > Explicitly Solvated Large Systems", Int. J. Quant. Chem., 2009, 109, > 15, 3781-3790) come to mind. The nudged elastic band method, in > particular, might be a good place to start, since you have initial and > final structures. > > To my knowledge, none of these is implemented directly within GROMACS, > but all could be implemented using GROMACS as a dynamics backend. > (NEB > > On Wed, Apr 18, 2012 at 2:26 AM, neeru sharma > wrote: > > Dear Gromacs users, > > > > > > I am simulating a system containing Protein-Mg-GDP and Protein-Mg-GTP > using > > Gromacs. I have already carried out classical MD simulation for the > > Protein-Mg-GDP complex. Then, I replaced GDP with GTP in the complex and > now > > have to analyse the structural changes in the Protein-Mg-GTP complex > during > > the simulation. I tried to perform classical MD simulation for the > > Protein-Mg-GTP complex too. But, as GDP to GTP state transition is a > > millisecond time-scale event, through classical MD, it seems practically > > impossible to achieve this time-scale transition. > > > > I already have the crystal structure available with me for the > > Protein-Mg-GTP complex. > > As, I am new to gromacs, can anybody suggest me any method to perform > this > > transition using some accelerated molecular dynamics method available > with > > gromacs and how it can be performed for my system? > > > > > > Any help will be highly appreciated. > > > > Thanks in advance > > > > - > > Neeru Sharma, > > Pune (India) > > > > -- > -- 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] Flooding approach and parameters for protein system
Dear gromacs users, I am a gromacs user and need some help regarding the implementation of flooding approach in gromacs. I am simulating a system containing Protein-Mg-GDP and Protein-Mg-GTP using Gromacs which is a 166 residue protein+mg+GTP/GDP complex. I have already carried out classical MD simulation for the Protein-Mg-GDP complex. Then, I replaced GDP with GTP in the complex and now have to analyse the structural changes in the Protein-Mg-GTP complex during the simulation. I tried to perform classical MD simulation for the Protein-Mg-GTP complex too. But, as GDP to GTP state transition is a millisecond time-scale event, through classical MD, it seems practically impossible to achieve this time-scale transition. I was looking for the methods available in gromacs that can accelerate this event. I was reading a paper titled: " Flooding in GROMACS: Accelerated Barrier Crossings in Molecular Dynamics". I have some queries with respect to the above matter. 1) Can we manually specify simulation length when performing "Flooding simulation", that we want to finish the simulation in the given specified time duration? 2) Can we specify reaction coordinates (Eg: The RMSD with the desired output state, Specific H-bonding or distance pattern etc) for the flooding simulation, as I already have the crystal structure available with me for the Protein-Mg-GTP complex (output state desired to be achieved with the simulation). 3) How to set the parameter values for Eflnull, tau and deltaFO in flooding for a protein system ? As, I am new to gromacs, can you please help me regarding the above mentioned matter and how it can be approached with my system? Any help will be highly appreciated. Regards, Neeru Sharma -- 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] Methods for accelerated MD simulation for Protein-Mg-GTP system in gromacs
Dear Gromacs users, I am simulating a system containing Protein-Mg-GDP and Protein-Mg-GTP using Gromacs. I have already carried out classical MD simulation for the Protein-Mg-GDP complex. Then, I replaced GDP with GTP in the complex and now have to analyse the structural changes in the Protein-Mg-GTP complex during the simulation. I tried to perform classical MD simulation for the Protein-Mg-GTP complex too. But, as GDP to GTP state transition is a millisecond time-scale event, through classical MD, it seems practically impossible to achieve this time-scale transition. I already have the crystal structure available with me for the Protein-Mg-GTP complex. As, I am new to gromacs, can anybody suggest me any method to perform this transition using some accelerated molecular dynamics method available with gromacs and how it can be performed for my system? Any help will be highly appreciated. Thanks in advance - Neeru Sharma, Pune (India) -- 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] Protein-MG-GDP (Protein-Ion-ligand) system simulation
Dear Gromacs users, I have to simulate a system consisting of Protein+MG+GDP where Protein is in complex with MG and GDP. I generated the GDP parameters using antechamber and then converted the topology,coordinate and parameter files to the corresponding gromacs format. Then, I tried to start with the simulation using AMBER ff03 forcefield. The system ran well till energy minimization step, but at equilibration steps it is showing lincs error at NVT equilibration step. I used 2 coupling groups for my system with lincs constraint algorithm as follows: *tc-grps = Protein_MG_GDP Water_and_ions * I tried turning off lincs warning too, den NVT equilibration was done finely but the system was blowing up during NPT equilibration. I tried with 3-4 steps of minimization also, but it didnt work (I have tried with lincs warning off in NPT too). I have visualized the NVT output trajectory and compared it with the initial structure too, and the trajectory was fine. I am unable to figure out the reason for why the system is blowing up. I am following the drug-ligand simulation tutorial but still can't figure out the problem. Can anyone suggest any possible means to overcome this situation? If anyone has simulated any similar system with Protein-ion-ligand complex or have faced similar problem, please share with what to do now to resolve this issue or to simulation such a system? Any help will be highly appreciated. Thanks - Neeru Sharma, Pune (India) -- 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: Coupling groups for nvt equilibration
Thanks Justin. I have tried both ways now and considering Protein_MG_GDP and Water_ions groups, it is running without any error but Protein_GDP and MG_Water_ions is failing with an error message. Thanks again... Neeru > > neeru sharma wrote: > > > > > > Thanks Justin. > > > > I tried the simulation with Protein_GDP and Water_ions, considering that > > "Water_and_ions" group will include MG. But it didn't work showing an > > error,saying "One atom not present in the coupling group". Shall I try > > to include MG in Water_ions group via make_ndx ? > > > > I think the better approach is the one you posted before. > > -Justin > > > > > > > Neeru > > > > neeru sharma wrote: > > > Dear Gromacs users, > > > > > > > > > I am simulating a system containing a protein with covalently > > attached > > > Mg in complex with GDP. > > > > > > For nvt equilibration, I have taken protein+Mg+GDP as the single > > group > > > and Water+ions as the other. The corresponding block from the > > .mdp file > > > is below: > > > > > > -- ; Temperature coupling is on > > > tcoupl = V-rescale > > > tc-grps = Protein_MG_GDP Water_and_ions > > > > > > > > > > > > Is this coupling method correct, to treat Protein and Mg as > different > > > quantities? > > > > > > > You are not treating them differently; they are in a merged group. > > Note, > > though, that the default "Water_and_ions" group will include MG, and > > thus grompp > > with throw a fatal error. You'll have to create a custom group for > > this one, as > > well. Otherwise, the approach seems reasonable to me. > > > > -Justin > > > > -- > > > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > -- gmx-users mailing listgmx-users@gromacs.org 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: Coupling groups for nvt equilibration
Thanks Justin. I tried the simulation with Protein_GDP and Water_ions, considering that "Water_and_ions" group will include MG. But it didn't work showing an error,saying "One atom not present in the coupling group". Shall I try to include MG in Water_ions group via make_ndx ? Neeru neeru sharma wrote: > > Dear Gromacs users, > > > > > > I am simulating a system containing a protein with covalently attached > > Mg in complex with GDP. > > > > For nvt equilibration, I have taken protein+Mg+GDP as the single group > > and Water+ions as the other. The corresponding block from the .mdp file > > is below: > > > > -- ; Temperature coupling is on > > tcoupl = V-rescale > > tc-grps = Protein_MG_GDP Water_and_ions > > > > > > > > Is this coupling method correct, to treat Protein and Mg as different > > quantities? > > > > You are not treating them differently; they are in a merged group. Note, > though, that the default "Water_and_ions" group will include MG, and thus > grompp > with throw a fatal error. You'll have to create a custom group for this > one, as > well. Otherwise, the approach seems reasonable to me. > > -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
[gmx-users] Coupling groups for nvt equilibration
Dear Gromacs users, I am simulating a system containing a protein with covalently attached Mg in complex with GDP. For nvt equilibration, I have taken protein+Mg+GDP as the single group and Water+ions as the other. The corresponding block from the .mdp file is below: -- ; Temperature coupling is on tcoupl = V-rescale tc-grps = Protein_MG_GDP Water_and_ions Is this coupling method correct, to treat Protein and Mg as different quantities? Thanks --- Neeru Sharma Pune (India) -- 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: Re: [gmx-users] Problem with GDP parameters generation
Thanks Mark for the response. I have contacted the amber mailing list too and I have got the parameters for GDP in AMBER94 forcefield. But I would need the parameters in AMBER03 forcefield, so that I can use them while running simulations in gromacs. So, can I use the same parameters of AMBER94 in AMBER03 too? Neeru > > On 10/12/2011 6:25 AM, neeru sharma wrote: > > Dear gromacs users, > > > > I have to simulate a protein-GDP complex using gromacs.As PRODRG was > > giving unreliable output, I generated Amber topology and coordinate > > files for GTP molecule. Then, I converted them into the corresponding > > gromacs topology (.top) and coordinate files (.gro) and generated > > parameter (.itp) file using following command (Thanks to Tsjerk): > > sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e > > '/^\s*\[\s*moleculetype\s*\]\s*$/,$p' TOP > ITP > > > > But the topology and co-ordinates file are quite different from the > > input PDB file and hence the parameters are also faulty, the GDP > > molecule is not fitting in the binding pocket of protein. Upon > > tracking the whole process, it was found that the error might be while > > using antechamber for generating prepin file using Gaussian output > > file as the input. > > > > Can anyone please suggest some way to apply some constraints in the > > antechamber command itself. OR if anybody has the paramters or > > topology for GDP, can anyone provide me the same so that I can compare > > and see where the parameters are differing. > > Surely antechamber will accept whatever coordinate file you provide to > it, and the AMBER mailing list is the place to make inquiries about it > (after checking the documentation). > > Don't stress too much about the charges - those that are suitable in the > bound and unbound form will normally be different, and current methods > can't access the former. > > Mark > -- next part -- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20111210/8550a169/attachment-0001.html > > -- 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 GDP parameters generation
Dear gromacs users, I have to simulate a protein-GDP complex using gromacs.As PRODRG was giving unreliable output, I generated Amber topology and coordinate files for GTP molecule. Then, I converted them into the corresponding gromacs topology (.top) and coordinate files (.gro) and generated parameter (.itp) file using following command (Thanks to Tsjerk): sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e '/^\s*\[\s*moleculetype\s*\]\s*$/,$p' TOP > ITP But the topology and co-ordinates file are quite different from the input PDB file and hence the parameters are also faulty, the GDP molecule is not fitting in the binding pocket of protein. Upon tracking the whole process, it was found that the error might be while using antechamber for generating prepin file using Gaussian output file as the input. Can anyone please suggest some way to apply some constraints in the antechamber command itself. OR if anybody has the paramters or topology for GDP, can anyone provide me the same so that I can compare and see where the parameters are differing. Thanks Neeru Sharma Pune (India) -- 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] .top to .itp file conversion
Dear gromacs users, I have generated Amber topology and coordinate files for GTP molecule. Then, I converted them into the corresponding gromacs topology (.top) and coordinate files (.gro). Now, I need to convert this gromacs .top file into .itp format. Is there any command in gromacs or any other tool to do so. Thanks Neeru Sharma CDAC, Pune (India) -- 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
