GROMACS version:2018
Hi dear users,
I want to perform MD simulation on a protein containing 3 Zn ions by amber99sb force field.by -his and CYM and applying distance restraint, zn ions fixed in their position with out any movement but after energy minimization I got the bellow warnings,now I do not know how to change nvtmdp parameters number to solve the problem.
''WARNING 1 [file topol.top, line 86896]:
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_ZN is 18332.72
Number of degrees of freedom in T-Coupling group NA_CL_Water is 177762.28
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K
Calculated rlist for 1x1 atom pair-list as 0.935 nm, buffer size 0.035 nm
Set rlist, assuming 4x4 atom pair-list, to 0.900 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 64x72x60, spacing 0.151 0.155 0.158
Estimate for the relative computational load of the PME mesh part: 0.19
This run will generate roughly 8 Mb of data’’
Hi,
how did you restraint the ZN distance?
I sugget to restrain using an harmonic potential (func 6 in table http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html?highlight=force%20field%20table).
Previously for Zn-N(HIS) I have use this setting : 0.207 for b0 and 4000 for k0 together with funct 6, and it works well
Best regards
Alessandra
Hi Dear Alevilla,
Thanks for your respose.and for cystein what should I do? and my distance restraint is:
distance_restraints ]
; ai aj type index type’ low up1 up2 fac
9215 745 1 0 1 0.0 0.3 0.4 1.0
9215 800 1 0 1 0.0 0.3 0.4 1.0
9215 1054 1 0 1 0.0 0.3 0.4 1.0
9215 1098 1 0 1 0.0 0.3 0.4 1.0
9216 218 1 1 1 0.0 0.3 0.4 1.0
9216 245 1 1 1 0.0 0.3 0.4 1.0
9216 477 1 1 1 0.0 0.3 0.4 1.0
9216 561 1 1 1 0.0 0.3 0.4 1.0
9217 53 1 2 1 0.0 0.3 0.4 1.0
9217 98 1 2 1 0.0 0.3 0.4 1.0
9217 375 1 2 1 0.0 0.3 0.4 1.0
Hi,
the distance restraints you are using are developed to account for NMR data. If you want to use them, I suggest to tune the values for your specific case.
See here more details on distance restraint
I suggest to use simple distance restraints (option 1 in the manual). For Zn distance you can take for example an values of the Zn-X that is observed experimentally.
Best regards
Alessandra
Hi,
I tried harmonic potential too and also change my distance restraint but again faced with those warnings that I was mentioned in my post.as my em.gro is ok can I continue with maxwarn? I do not understand where is the problem!
Hi,
I see. The warning is not connected with the Zn, but to the use of constraints. With AMBER force field use constraint only the h-bonds, to be in line with the force field parameterization.
best regards
Alessandra
I try It even with out distance_restraint,but again I was faced with this warnings
Hi,
What I meant that the warning is not related to distance restraint, but to the constraints definition, that you use in mdp file. My guess is that you use all-bonds, but the warning suggests to use h-bonds (as option).
See http://manual.gromacs.org/current/user-guide/mdp-options.html#bonds
Best regards
Alessandra
Hi,
my problem was solved by harmonic potential.now for calculating RMSD I get this error:
WARNING: Masses and atomic (Van der Waals) radii will be guessed
based on residue and atom names, since they could not be
definitively assigned from the information in your input
files. These guessed numbers might deviate from the mass
and radius of the atom type. Please check the output
files if necessary.
Can not find mass in database for atom ZN in residue 702 ZN
Can not find mass in database for atom ZN in residue 703 ZN
Can not find mass in database for atom ZN in residue 704 ZN
I added zn atoms in index now I do not know which part of my index has a problem?
The database is case-sensitive. Change ZN to Zn and it should match the element entry.