Hello Everyone,
I have solved this problem. However,i would like to ask how can I make an index file for Temperature Coupling for Protein_Zn_Ligand? When i tried to make the index group for the Protein_Zn_Ligand and I got the following error. Is the nvt simulation correct if i don't add Zn to the Temperature Coupling?
Program: gmx grompp, version 2019.1
Source file: src/gromacs/gmxpreprocess/readir.cpp (line 2667)
Fatal error:
Atom 4265 in multiple T-Coupling groups (1 and 2)
The nvt parameters are mentioned below:
title = Protein-ligand complex NVT equilibration
define = -DPOSRES -DPOSRES_LIG ; position restrain the protein and ligand
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 30000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps #include
nstxout-compressed = 500 ; save coordinates every 1.0 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds to H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighbor searching and vdW
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 20 ; largely irrelevant with Verlet
rlist = 1.2
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_NAD Water_and_ions ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction is not used for proteins with the C36 additive FF
DispCorr = no
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
Please let me know if i am doing something wrong. Thanks for your time.
With kind regards,
Amit
11.10.2019, 12:09, "Amit Jaiswal" <amitja...@yandex.com>:
Dear Jorden,Thanks for reply. I followed your suggestions and i got an error as follows:Command line:gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tprIgnoring obsolete mdp entry 'title'Setting the LD random seed to 1403244422Generated 100032 of the 100128 non-bonded parameter combinationsGenerating 1-4 interactions: fudge = 1Generated 65937 of the 100128 1-4 parameter combinationsERROR 1 [file posre_zn.itp, line 5]:Atom index (2220) in position_restraints out of bounds (1-1).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.-------------------------------------------------------Program: gmx grompp, version 2019.1Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1818)Fatal error:There was 1 error in input file(s)I guess there is something wrong with my topology file but i am unable to figure it out.My topology file looks like this:; Include Position restraint file#ifdef POSRES#include "posre.itp"#endif; Include ligand topology#include "nad.itp"; Ligand position restraints#ifdef POSRES_LIG#include "posre_nad.itp"#endif; Include water topology#include "./charmm36-mar2019.ff/tip3p.itp"#ifdef POSRES_WATER; Position restraint for each water oxygen[ position_restraints ]; i funct fcx fcy fcz1 1 1000 1000 1000#endif; Include topology for ions#include "./charmm36-mar2019.ff/ions.itp"#ifdef POSRES#include "posre_zn.itp"#endif[ system ]; NameProtein in water[ molecules ]; Compound #molsProtein_chain_A 1ZN 1NAD 1SOL 12908NA 4Would you please let me know my mistake. Thanks for your time.With kind regards,Amit10.10.2019, 15:41, "Jorden Cabal" <jordenca...@gmail.com>:> Hi Amit,> The metal ion needs to be treated very very carefully so as to maintain> their co-ordination state with the nearby atoms of protein.> To do this, one needs to generate the parameter separately for the complex> formed by the metal ion with the protein residues because due to presence> of metal ion in the vicinity, the residues nearby will have different> parameters than other proteins especially the charge distribution. One> method of incorporating this model is to model the metal ion as a> dummy-particle metal ion complex model where the dummy particles carry some> partial charge and the whole complex represent the co-ordination state of> that particular atom.> I would suggest you to go through this paper>> In case, you do not want to go in that much detailed modeling of metal ion> for your system, which I think is very important to study metalloproteins,> another very simple method of solving the problem you are facing is to> treat metal ions as single sphere as you are treating in your system. To> avoid its displacement from its location, you need to apply some distance> restraints which is very easy to apply in Gromacs.> You can create the distance restraint using "*genrestr*" command. Please> note that applying any kind of restraint will definitely add some bias to> your simulation.> Thank you>> On Thu, Oct 10, 2019 at 1:05 PM Amit Jaiswal <amitja...@yandex.com> wrote:>>> Hello Everyone,>>>> Would you please let me know what should we do when the zinc ion gets>> displaced during simulation of a Protein-Zn-Ligand complex? What are the>> possible options one can perform under such conditions? If possible, please>> mention the steps needed to be performed briefly as i am new to GROMACS.>> Your suggestions will help me a lot and thanks in advance.>>>> With kind regards,>> Amit>> -->> Gromacs Users mailing list>>>> * Please search the archive at>> posting!>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists>>>> * For (un)subscribe requests visit>> 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.,--
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