[gmx-users] some question about REMD

[Albert]

Hello Justine:

I've got the following messages by command:

  grompp -f implicit.mdp -c complex.pdb -p complex.top -o test.tpr

Setting gen_seed to 18463
Velocities were taken from a Maxwell distribution at 310 K

GB parameter(s) missing or negative for atom type 'OS'

-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 1123

Fatal error:
Can't do GB electrostatics; the implicit_genborn_params section of the 
forcefield is missing parameters for 1 atomtypes or they might be negative.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"Uh-oh .... Right Again" (Laurie Anderson)

thank you very much
best
Albert



On 10/17/2012 07:58 PM, Justin Lemkul wrote:
>
>
> On 10/17/12 1:52 PM, Albert wrote:
>> Hi Justin:
>>
>> Thank you very much for eply.
>>
>> So the modified .mdp file (including the GBSA model setting) is the 
>> following?
>> Is this correct?
>>
>
> No.  See inline comments.
>
>> title = Protein-ligand complex NVT equilibration
>> define = -DPOSRES ; position restrain the protein and ligand
>
> There is no need for restraints.  There is no solvent to equilibrate 
> around the protein.
>
>> ; Run parameters
>> integrator = sd ;
>> nsteps = 50000 ; 2 * 50000 = 100 ps
>> dt = 0.002 ; 2 fs
>> nstxout = 100 ; save coordinates every 0.2 ps
>> nstvout = 100 ; save velocities every 0.2 ps
>> nstenergy = 100 ; save energies every 0.2 ps
>> nstlog = 100 ; update log file every 0.2 ps
>> energygrps = Protein JZ4
>
> This is only appropriate if you're following the tutorial exactly.  
> From your previous description, you are dealing with a protein and no 
> ligand.
>
>> ; Bond parameters
>> continuation = no ; first dynamics run
>> constraint_algorithm = lincs ; holonomic constraints
>> constraints = all-bonds ; all bonds (even heavy atom-H bonds) 
>> constrained
>> lincs_iter = 1 ; accuracy of LINCS
>> lincs_order = 4 ; also related to accuracy
>> ; Neighborsearching
>> ns_type = grid ; search neighboring grid cells
>
> You need ns-type = simple.
>
>> nstlist = 5 ; 10 fs
>
> Set nstlist = 0 for a fixed neighbor list.  In conjunction with 
> infinite cutoffs, you will use the all-vs-all kernels, which are 
> highly optimized.
>
>> rlist = 0 ; short-range neighborlist cutoff (in nm)
>> rcoulomb = 0 ; short-range electrostatic cutoff (in nm)
>> rvdw = 0 ; short-range van der Waals cutoff (in nm)
>> ; Electrostatics
>> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
>
> Set coulombtype = cutoff.
>
>> pme_order = 4 ; cubic interpolation
>> fourierspacing = 0.16 ; grid spacing for FFT
>> ; Temperature coupling
>> tcoupl = V-rescale ; modified Berendsen thermostat
>
> Note that tcoupl is ignored when using the sd integrator.
>
>> tc-grps = Protein_JZ4 Water_and_ions ; two coupling groups - more 
>> accurate
>
> You don't have water and ions in an implicit system, and likely you 
> don't have a ligand.
>
>> tau_t = 0.1 0.1 ; time constant, in ps
>
> tau_t is too low for sd, use something like 1.0.
>
>> 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=no
>> ; Dispersion correction
>> DispCorr = EnerPres ; account for cut-off vdW scheme
>
> Unnecessary with infinite cutoffs.
>
>> ; Velocity generation
>> gen_vel = yes ; assign velocities from Maxwell distribution
>> gen_temp = 300 ; temperature for Maxwell distribution
>> gen_seed = -1 ; generate a random seed
>>
>> ; IMPLICIT SOLVENT ALGORITHM
>> implicit_solvent = yes
>>
>> ; GENERALIZED BORN ELECTROSTATICS
>> ; Algorithm for calculating Born radii
>> gb_algorithm = OBC
>> ; Frequency of calculating the Born radii inside rlist
>> nstgbradii = 1
>
> This should also be set to zero.
>
>> ; Cutoff for Born radii calculation; the contribution from atoms
>> ; between rlist and rgbradii is updated every nstlist steps
>> rgbradii = 5
>
> Set to zero.
>
> -Justin
>
>> ; Dielectric coefficient of the implicit solvent
>> gb_epsilon_solvent = 80
>> ; Salt concentration in M for Generalized Born models
>> gb_saltconc = 0
>> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
>> gb_obc_alpha = 1
>> gb_obc_beta = 0.8
>> gb_obc_gamma = 4.85
>> gb_dielectric_offset = 0.009
>> sa_algorithm = Ace-approximation
>> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of 
>> GBSA
>> ; The value -1 will set default value for Still/HCT/OBC GB-models.
>> sa_surface_tension = -1
>>
>>
>>
>> On 10/17/2012 07:45 PM, Justin Lemkul wrote:
>>>
>>>
>>> On 10/17/12 1:43 PM, Albert wrote:
>>>> hello Justin:
>>>>
>>>> thanks a lot for kind reply.
>>>> I've got another question: how to disable PBC? shall I simply 
>>>> delete "pbc=xyz"
>>>> from .mdp file? I found that sometimes if we delete some parameters 
>>>> from .mdp,
>>>> gromacs will use the default instead of disable it.
>>>>
>>>
>>> The default setting for pbc is xyz, so deleting the line 
>>> accomplishes nothing.
>>> Set "pbc = no" in the .mdp file.
>>>
>>> -Justin
>>
>