Re: [gmx-users] Umbrella sampling along a dihedral angle
On 12/27/14 1:50 PM, Nash, Anthony wrote: Hi Justin, I think I've shot myself in the foot and I'm trawling the gromacs manual with little success at the moment. I'm trying to define my [ dihedral_restraint ] over my ligand-enzyme complex. The topology of the ligand is in one .itp file and the topology of the enzyme is in a separate .itp file. Therefore, in my top level topology file (system.top) I have: #include "../enzyme.itp" #include "../ligand.itp" Typically if I want restraints to help equilibrate the system I would just define a posre_NAME.itp with the respective force constants beneath each #include directive. But given that each topology file starts with atom 1 I am a bit unsure how I can define a set of restraints over two topology files. Can this be done? I'm really hoping I won't need to clump all topologies into one big file. Restraints are always numbered with respect to the [moleculetype] to which they apply. As an example: http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds If your (pseudo)dihedral spans the protein and the ligand, the only way to proceed with a restraint is to have a merged [moleculetype] of protein and ligand. They simply cannot be in separate topologies in this case. -Justin Thanks as ever, Anthony Dr Anthony Nash Department of Chemistry University College London From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 27 December 2014 14:49 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling along a dihedral angle On 12/26/14 6:11 PM, Nash, Anthony wrote: Dear Gromacs community, Using enforced rotation potentials I have generated a really smooth rotation of my ligand the catalytic binding domain of my protein. I then put together a simple perl script to calculate the dihedral angle of four particular atoms at each time step using g_angle. Taking a 6 degree interval (for a total of 60 windows to span the 360 degree rotation) I modified the topology with a [ dihedral_restraint ] with the respective dihedral angle for that particular configuation. I plan on then running each window for 10 ns to begin with (according to the PMF profile I can add more time). It is from this point where I am a little stuck. I have gone through a number of posts going back to 2011 with regards to using umbrella sampling along a dihedral angle reaction coordinate. The precise post was from Justin: "You'll have to build various configurations that correspond to different dihedral angles (which form the sampling windows), then restrain them. The energy attributed to the restraints is then stored in the .edr file. From these energies, you should be able to construct the energy curve over the sampling windows. There are examples of this in the literature, so I suspect you should be able to find some demonstrations of how it's applied." I was wondering whether gromacs now support this procedure natively? I noticed g_wham has an option -cycl for dihedrals but I am still not sure how this fits in with the traditional gromacs means of generating pull force output as I have only been using distance based rather than angular based umbrella sampling. g_wham is still only really designed to process the output from the pull code, not any generalized restraint. That would be a nice features, but AFAIK it is not in the pipeline. You can de-bias the results like I suggested above, but it's probably more work than it's worth. I would suggest just using Alan Grossfield's WHAM implementation. There, you just need to provide the raw numbers (in this case, the dihedral values) and the force constants used. It will then give you your PMF. We have done this recently; it is very easy. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbank
Re: [gmx-users] charge distribution
On 12/27/14 3:54 PM, elham tazikeh wrote: Dear gromacs users i d like to know about charge distribution in .itp file that how can fix the charge of atoms for instance, i simulated Aspirin in Human serum albumin, and i want to know about their charges in an article charge distribution was as below, but in my .itp file (aquired by PRODRG server) i had 11 atoms instead of 13 atoms Neither is enough atoms for aspirin, which should have 17 atoms in its united-atom representation (explicit H on aromatic C). Aspirin would have 13 atoms if the aromatic H are not explicit (wrong for Gromos96). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] core dumped
On 12/27/14 4:22 PM, elham tazikeh wrote: Dear Justin thanks for your advise only my remained question is, if my problem was for my topology file (as i recieved this error a few times: your topology file has non-zero charge = -0.61) by editing my topology file (.itp file), can i going on my simulation? Whatever editing you did was wrong if you end up with such a horrendous fractional charge. please tell me, what is the best way for distribute the charges on a molecule (Aspirin)? All of the necessary functional groups are available in the Gromos force field (presumably that's what you're after since you were using PRODRG); the aromatic ring and carboxylic acid are standard components of the protein force field and the methyl ester group has had its parameters published recently. For Gromos force fields, the transferability is very good, you usually just need to piece together existing groups. For a drug molecule, a partition coefficient is likely readily available and serves as an excellent experimental target datum for verifying that your topology is reasonable. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Umbrella sampling along a dihedral angle
Hi Justin, Thanks for the reply, always appreciated. I like the way gromacs can handle modular structures by breaking up the topology into separate .itp file. Unfortunately this is the first time I've had to span two subunits with a specific restraint. I quickly knocked together a perl script to combine .itp topology files, and now it's all working fine. Thanks again. Anthony Dr Anthony Nash Department of Chemistry University College London From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 28 December 2014 19:57 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling along a dihedral angle On 12/27/14 1:50 PM, Nash, Anthony wrote: > Hi Justin, > > I think I've shot myself in the foot and I'm trawling the gromacs manual with > little success at the moment. I'm trying to define my [ dihedral_restraint ] > over my ligand-enzyme complex. The topology of the ligand is in one .itp file > and the topology of the enzyme is in a separate .itp file. Therefore, in my > top level topology file (system.top) I have: > > #include "../enzyme.itp" > #include "../ligand.itp" > > Typically if I want restraints to help equilibrate the system I would just > define a posre_NAME.itp with the respective force constants beneath each > #include directive. But given that each topology file starts with atom 1 I am > a bit unsure how I can define a set of restraints over two topology files. > > Can this be done? I'm really hoping I won't need to clump all topologies into > one big file. > Restraints are always numbered with respect to the [moleculetype] to which they apply. As an example: http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds If your (pseudo)dihedral spans the protein and the ligand, the only way to proceed with a restraint is to have a merged [moleculetype] of protein and ligand. They simply cannot be in separate topologies in this case. -Justin > Thanks as ever, > Anthony > > > > Dr Anthony Nash > Department of Chemistry > University College London > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin > Lemkul [jalem...@vt.edu] > Sent: 27 December 2014 14:49 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Umbrella sampling along a dihedral angle > > On 12/26/14 6:11 PM, Nash, Anthony wrote: >> Dear Gromacs community, >> >> Using enforced rotation potentials I have generated a really smooth rotation >> of my ligand the catalytic binding domain of my protein. I then put together >> a simple perl script to calculate the dihedral angle of four particular atoms >> at each time step using g_angle. Taking a 6 degree interval (for a total of >> 60 windows to span the 360 degree rotation) I modified the topology with a [ >> dihedral_restraint ] with the respective dihedral angle for that particular >> configuation. I plan on then running each window for 10 ns to begin with >> (according to the PMF profile I can add more time). It is from this point >> where I am a little stuck. >> >> I have gone through a number of posts going back to 2011 with regards to >> using umbrella sampling along a dihedral angle reaction coordinate. The >> precise post was from Justin: >> >> "You'll have to build various configurations that correspond to different >> dihedral angles (which form the sampling windows), then restrain them. >> >> The energy attributed to the restraints is then stored in the .edr file. From >> these energies, you should be able to construct the energy curve over the >> sampling windows. There are examples of this in the literature, so I suspect >> you should be able to find some demonstrations of how it's applied." >> >> I was wondering whether gromacs now support this procedure natively? I >> noticed g_wham has an option -cycl for dihedrals but I am still not sure how >> this fits in with the traditional gromacs means of generating pull force >> output as I have only been using distance based rather than angular based >> umbrella sampling. >> > > g_wham is still only really designed to process the output from the pull code, > not any generalized restraint. That would be a nice features, but AFAIK it is > not in the pipeline. You can de-bias the results like I suggested above, but > it's probably more work than it's worth. I would suggest just using Alan > Grossfield's WHAM implementation. There, you just need to provide the raw > numbers (in this case, the dihedral values) and the force constants used. It > will then give you your PMF. We have done this recently; it is very easy. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Scien
[gmx-users] Fatal error during entropy calculation using g_anaeig
Hi all, I am trying to calculate entropy using g_anaeig (Gromacs version 5.0.1), after using g_nmeig to calculate eigenvectors and eigenvalues (after computing hessian matrix): g_nmeig_mpi -f hessian.mtx -s run.tpr -nom g_anaeig_mpi -v eigenvec.trr -entropy But I am getting the following error: Fatal error: Can not calculate entropies from mass-weighted eigenvalues, redo the analysis without mass-weighting. -- Thanks and Regards, Bipin Singh -- 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] charge distribution
Dear Justin i really appricite for your help i want to tell all did work until now, again: 1.total charges in my topol.top was +2, then by genion, i added 2 CL to my comlex (HSA+Aspirin) 2.My .itp file (produce by PRODRG) was(consist of 11 atoms) : [ moleculetype ] ; Name nrexcl SAL 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 SAL O1' 1 -0.765 15.9994 ;' 2 C 1 SAL C1' 10.354 12.0110 ;' 3OM 1 SAL O2' 1 -0.765 15.9994 ;' 4 C 1 SAL C1 1 -0.027 12.0110 5 CH2 1 SAL C6 10.102 14.0270 6 CH2 1 SAL C5 10.101 14.0270 7 CR1 1 SAL C4 20.010 13.0190 8 CR1 1 SAL C3 20.010 13.0190 9 C 1 SAL C2 20.130 12.0110 10OA 1 SAL O2 2 -0.191 15.9994 11 H 1 SAL H2 20.041 1.0080 with topology file and .itp file, after grompp (for produce nvt.tpr) i encounted to below error : *system has non-zero total charge : -0.61* 3.as yor re mentioned, Aspirin has 17 atoms. for charge distribution, i used of QM (NBO calculation) and my results was: 1 C -0.095205 2 C -0.077566 3 C -0.084684 4 C -0.028579 5 C -0.223106 6 C0.198041 7 H0.147099 8 H0.106100 9 H 0.101762 10 H 0.117238 11 C 0.443312 12 O -0.318010 13 H0.247465 14 O -0.341986 15 O -0.318846 16 C0.312765 17 O -0.320346 18 C -0.281115 19 H0.136126 20 H0.139768 21 H0.139765 these are estimated for* 2-acetoxy benzoic acid *alone (i dont know , must be calculate for complex HSA+Aspirin or Aspirin alone?) 4. on the other hand, i tried to search in *aminoacids.rtp* file for *gromos* force field , but saw only charges for ACE group(other aminoacids and some solvents) and i could not find out the charges of all atoms in Aspirin molecule. Overall, in your opinion, where is my problem? i m looking forward to seeing your advise cheers -- 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 remove water molecule inside micelle?
Dear gromacs users I prepared my simulation system containing SDS. Then I added water molecules using genbox. Some water molecules entered in to the micelle. How to remove water molecules inside the micelle? Any help will highly appreciated. -- 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.
