Re: [gmx-users] How to parametrize a new molecule?
Hello Herbert, Not related to your question, but be careful if you are going to use CHARMM36 force field for DNA, as a recent study ( https://pubs.acs.org/doi/10.1021/acs.jpcb.9b09106) shows that this ff does not preserve DNA stability at a longer time scale, in case you are going to do so. Best, Mahdi On Sat, Apr 4, 2020 at 3:21 AM Herbert de Castro Georg wrote: > Thanks, Justin! > > > > Em sex., 3 de abr. de 2020 às 22:15, Justin Lemkul > escreveu: > > > > > > > On 4/3/20 9:12 PM, Herbert de Castro Georg wrote: > > > Dear users, > > > > > > I want to perform a simulation of a molecule inside DNA. I'm probably > > going > > > to use CHARMM for DNA. But how do I parametrize the molecule? > > > > http://cgenff.umaryland.edu/ > > > > -Justin > > > > -- > > == > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalem...@vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > == > > > > -- > > 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. > > > -- > 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. -- 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] -t option?
Hi Hadi, It is well explained in Gromacs tutorial, in the below: http://www.mdtutorials.com/gmx/lysozyme/07_equil2.html "Note that we are now including the -t flag to include the checkpoint file from the *NVT* equilibration" Cheers, Mahdi On Wed, Sep 18, 2019 at 5:43 PM Hadi Rahmaninejad wrote: > Hello dear users, > > I am going to run a simulation according to a tutorial, but there is an > option of "-t nvt.cpt" that I don't know what is it, and I couldn't find > any explanation for that. I appreciate if any of you can give me a short > description of what is that doing, > > Best wishes, > Hadi > -- > 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. > -- 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] Constraints Error; In Using Tetrahedral Zinc Dummy Model
Dear Gromacs users, I am trying to simulate a zinc-finger protein in explicit water, *with CHARMM36 FF*. Unfortunately, I did not find any *tetrahedral zinc force* field in Gromacs and therefore I converted the tetrahedral dummy zinc model used in CHARMM27 FF to the format of Gromacs. The minimization of the system goes perfect but unfortunately when I start *NVT simulation*, I get this error: WARNING 1 [file topol.top, line 57]: The bond in molecule-type Dummy_chain_X between atoms 2 DZ1 and 3 DZ2 has an estimated oscillational period of 6.1e-03 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. ... Too many warnings (1). If you are sure all warnings are harmless, use the -maxwarn option. --- Here, DZ1 and DZ2 are dummy atoms related to tetrahedral zinc model. *in mdp file*, I have used *h-bonds* *Lincs* constraint. When I use the *all-bond* in the mdp file again I get another error that is: --- WARNING 1 [file topol.top, line 57]: There are atoms at both ends of an angle, connected by constraints and with masses that differ by more than a factor of 13. This means that there are likely dynamic modes that are only very weakly coupled. To ensure good equipartitioning, you need to either not use constraints on all bonds (but, if possible, only on bonds involving hydrogens) or use integrator = sd or decrease one or more tolerances: verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >= 4 or SHAKE tolerance <= 1e-05 Number of degrees of freedom in T-Coupling group Protein_DNA_ZNT is 6936.89 Number of degrees of freedom in T-Coupling group Water_and_ions is 179547.11 Does this error mean that I need to constraint zinc bonds beside h-bonds? If so, how should I do it? or something wrong in my topology is? *I will appreciate* if you let me know any idea to fix this problem. Cheers, Mahdi -- 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] Constraints Error; In Using Tetrahedral Zinc Dummy Model
Dear Gromacs users, I am trying to simulate a zinc-finger protein in explicit water, *with CHARMM36 FF*. Unfortunately, I did not find any *tetrahedral zinc force* field in Gromacs and therefore I converted the tetrahedral dummy zinc model used in CHARMM27 FF to the format of Gromacs. The minimization of the system goes perfect but unfortunately when I start *NVT simulation*, I get this error: WARNING 1 [file topol.top, line 57]: The bond in molecule-type Dummy_chain_X between atoms 2 DZ1 and 3 DZ2 has an estimated oscillational period of 6.1e-03 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. ... Too many warnings (1). If you are sure all warnings are harmless, use the -maxwarn option. --- Here, DZ1 and DZ2 are dummy atoms related to tetrahedral zinc model. *in mdp file*, I have used *h-bonds* *Lincs* constraint. When I use the *all-bond* in the mdp file again I get another error that is: --- WARNING 1 [file topol.top, line 57]: There are atoms at both ends of an angle, connected by constraints and with masses that differ by more than a factor of 13. This means that there are likely dynamic modes that are only very weakly coupled. To ensure good equipartitioning, you need to either not use constraints on all bonds (but, if possible, only on bonds involving hydrogens) or use integrator = sd or decrease one or more tolerances: verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >= 4 or SHAKE tolerance <= 1e-05 Number of degrees of freedom in T-Coupling group Protein_DNA_ZNT is 6936.89 Number of degrees of freedom in T-Coupling group Water_and_ions is 179547.11 Does this error mean that I need to constraint zinc bonds beside h-bonds? If so, how should I do it? *I will appreciate* if you let me know any idea to fix this problem. Cheers, Mahdi -- 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] Minimization stops without reaching the requested precision Fmax < 1000
Dear Gromacs Users, I am trying to add the tetrahedral zinc atom dummy model into CHARMM36 force field in Gromacs. In my system, this dummy zinc interact with four Cystein residues (CYM). The parameters of the zinc are available in CHARMM format, which I used to use it in NAMD package. After adding appropriate parameters, when I do energy minimization, I get this 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). ... Steepest Descents converged to machine precision in 1045 steps, but did not reach the requested Fmax < 1000. Potential Energy = -1.5922652e+06 Maximum force = 3.2106902e+07 on atom 3526 Norm of force = 1.4857810e+05 Atom 3526 is dummy atom of zinc ion. The dummy parameters added in ffbonded.itp file are: -- ffbonded.itp ;zinc dummy model, bonds HK ZD 1 0.0900451872.00 HK HK 1 0.1470451872.00 ;zinc dummy model, angles HK ZD HK 5 109.50 460.24 0. 0.00 HK HK HK 560.00 460.24 0. 0.00 HK HK ZD 535.25 460.24 0. 0.00 ;zinc dummy model, dihedrals ZD HK HK HK 935.30 0.00 2 HK ZD HK HK 9 120.00 0.00 2 HK HK HK HK 970.00 0.00 2 --- ffnonbonded.itp ;zinc dummy model ZD3061.380.000 A 0.3100 0.1 HK 1 1.0080000.500 A 0. 0.0 = In contrast to Gromacs, when I do minimization in NAMD, there is no such an error in minimization. I should mention that I am using single precision platform of Gromacs. I would appreciate if you could share me in case you have some ideas about this problem. Cheers, Mahdi -- 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] Minimization stops without reaching the requested precision Fmax < 1000
Dear Gromacs Users, I am trying to add the tethrahedral zinc atom dummy model into CHARMM36 force field in Gromacs. In my system, this dummy zinc interact with four Cystein residues (CYM). The parameters of the zinc are available in CHARMM format, which I used to use it in NAMD package. After adding appropriate parameters, when I do energy minimization, I get this 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). ... Steepest Descents converged to machine precision in 1045 steps, but did not reach the requested Fmax < 1000. Potential Energy = -1.5922652e+06 Maximum force = 3.2106902e+07 on atom 3526 Norm of force = 1.4857810e+05 Atom 3526 is dummy atom of zinc ion. The dummy parameters added in ffbonded.itp file are: -- ffbonded.itp ;zinc dummy model, bonds HK ZD 1 0.0900451872.00 HK HK 1 0.1470451872.00 ;zinc dummy model, angles HK ZD HK 5 109.50 460.24 0. 0.00 HK HK HK 560.00 460.24 0. 0.00 HK HK ZD 535.25 460.24 0. 0.00 ;zinc dummy model, dihedrals ZD HK HK HK 935.30 0.00 2 HK ZD HK HK 9 120.00 0.00 2 HK HK HK HK 970.00 0.00 2 --- ffnonbonded.itp ;zinc dummy model ZD3061.380.000 A 0.3100 0.1 HK 1 1.0080000.500 A 0. 0.0 = In contrast to Gromacs, when I do minimization in NAMD, there is no such an error in minimization. I should mention that I am using single precision platform of Gromacs. I would appreciate if you could share me in case you have some ideas about this problem. Cheers, Mahdi -- 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] CHARMM36 in Gromacs :DNA terminus residues problem
Dear all, I am trying to do MD simulation on my protein-DNA system in *Gromacs* using *CHARMM36* force field (*2019 version*, downloaded from Mackerell web homepage). The DNA residue names start from DG5 ==> DC3 (in both DNA strand): Once I do *pdb2gmx* command, seems it does not correctly recognize DNA terminal residues (as defined by Justin Lemkul in .tdb files as 5TER and 3TER flags) and seems it treats DNA as a protein and hence I get this error: * * Start terminus *DG5*-1: *NH3+* End terminus *DC3*-21: *COO-* --- Program: gmx pdb2gmx, version 2018.4 Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1127) Fatal error: atom N not found in buiding block 1DG5 while combining tdb and rtp ** Unfortunately, I was not able to fix this error and therefore I will appreciate if someone could let me know how can I fix this problem. Cheers, Mahdi -- 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.
