[gmx-users] Very high energies after energy minimization
Deep Bhattacharya
hypergenetics at gmail.com
Wed Jul 27 22:30:34 CEST 2016
Would you suggest to do the minimization of protein and ligand in water or
vacuum?
Deep
On Wed, Jul 27, 2016 at 3:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/27/16 3:41 PM, Deep Bhattacharya wrote:
>
>> Hello Evan,
>>
>> I am using the SPC solvent model.
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ; i funct fcx fcy fcz
>> 1 1 1000 1000 1000
>> #endif
>>
>> Posre.itp from pdb2gmx for the protein
>> ; In this topology include file, you will find position restraint
>> ; entries for all the heavy atoms in your original pdb file.
>> ; This means that all the protons which were added by pdb2gmx are
>> ; not restrained.
>>
>> [ position_restraints ]
>> ; atom type fx fy fz
>> 1 1 1000 1000 1000
>> 5 1 1000 1000 1000
>> 6 1 1000 1000 1000
>> 7 1 1000 1000 1000
>> 8 1 1000 1000 1000
>> 9 1 1000 1000 1000
>> 10 1 1000 1000 1000
>> Cut out the initial part, remains constant throughout the same.
>>
>> Please suggest what changes can I do.
>>
>>
> mdrun tells you that an absurd force is acting on atom 1553. Open up the
> structure in your favorite visualization software and start looking there.
> Beyond that, follow
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>
> Try minimizing the protein alone, the ligand alone, etc. until you spot
> where the problem comes from.
>
> -Justin
>
>
> Sincerely,
>> Deep Bhattacharya
>>
>> On Wed, Jul 27, 2016 at 2:35 PM, Evan Lowry <evanwlowry at gmail.com> wrote:
>>
>> Something is seriously wrong with the system. Do you have a solvent? If
>>> so,
>>> use a trajectory viewer to ensure that there aren't solvent molecules on
>>> top of your protein for some reason. Otherwise, it is probably related to
>>> the protein structure clashing with itself (e.g., atoms are too close or
>>> charges are incorrect). Additionally, what is in your positional
>>> restraint
>>> file? Maybe you are arbitrarily restraining things that shouldn't be
>>> restrained. Those are some things to check.
>>>
>>> Evan L.
>>>
>>> On Wed, Jul 27, 2016 at 1:04 PM, Deep Bhattacharya <
>>> hypergenetics at gmail.com>
>>> wrote:
>>>
>>> Hello,
>>>>
>>>> I am attempting in performing energy minimization on
>>>> protein-carbohydrate
>>>> complex and I have obtained
>>>> *Energy minimization has stopped, but the forces have not converged to
>>>>
>>> the*
>>>
>>>> *requested precision Fmax < 1000 (which may not be possible for your
>>>> system).*
>>>> *It stopped because the algorithm tried to make a new step whose size
>>>> was
>>>> too*
>>>> *small, or there was no change in the energy since last step. Either
>>>> way,
>>>> we*
>>>> *regard the minimization as converged to within the available machine*
>>>> *precision, given your starting configuration and EM parameters.*
>>>> *You might need to increase your constraint accuracy, or turn*
>>>> *off constraints altogether (set constraints = none in mdp file)*
>>>>
>>>> *Steepest Descents converged to machine precision in 193 steps,*
>>>> *but did not reach the requested Fmax < 1000.*
>>>> *Potential Energy = -2.25884936387141e+13*
>>>> *Maximum force = 3.70136760562579e+25 on atom 1553*
>>>> *Norm of force = 2.39587460988866e+23*
>>>>
>>>>
>>>> ; minim.mdp - used as input into grompp to generate em.tpr
>>>> *define = -DPOSRES -DPOSRES_LIGAND*
>>>> *integrator = steep *
>>>> *emtol = 1000.0 *
>>>> *emstep = 0.001 *
>>>> *nsteps = 50000 *
>>>> *energygrps = System*
>>>> *nstlist = 1*
>>>> *constraints = none*
>>>> *; Parameters describing how to find the neighbors of each atom and how
>>>>
>>> to
>>>
>>>> calculate the interactions*
>>>> * ; Frequency to update the neighbor list and long range forces*
>>>> *ns_type = grid ; Method to determine neighbor list (simple, grid)*
>>>> *rlist = 1.0 ; Cut-off for making neighbor list (short range forces)*
>>>> *coulombtype = PME ; Treatment of long range electrostatic interactions*
>>>> *rcoulomb = 1.0 ; long range electrostatic cut-off*
>>>> *rvdw = 1.0 ; long range Van der Waals cut-off*
>>>> *pbc = xyz ;Periodic Boundary Conditions (yes/no)*
>>>> *em.mdp*
>>>>
>>>> The maximum force seems unrealistic, how can I solve this issue?
>>>> I have substituted charges of my ligand using atomicchargecalculator
>>>>
>>> (DOI:
>>>
>>>> 10.1186/s13321-015-0099-x-- ) in the original file from PRODRG server.
>>>> After reading many posts I can infer that there might be come problem in
>>>> the topology of the ligand or the protein but I am not to recognize the
>>>> actual source of the problem because if I go ahead with NPT and NVT
>>>> equilibration my system is just exploding.
>>>>
>>>> Please help.
>>>> Thanks in advance.
>>>> *Deep S Bhattacharya*
>>>> *Graduate Research Assistant*
>>>> Mohs Biomedical Imaging & Nanotechnology Group
>>>> Pharmaceutical Sciences
>>>> *University of Nebraska Medical Center*
>>>> 4018 Eppley Science Hall | Omaha, NE 68198-6805
>>>> office 402.559.4349 | cell 402.906.1640
>>>> deep.bhattacharya at unmc.edu.deep.bhattacharya199@gmail.com
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>>
>>
>>
> --
> ==================================================
>
> 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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--
Deep Bhattacharya.
Post-Graduate Student,
Department of Pharmaceutical Chemistry,
Bombay College Of Pharmacy.
Mobile - +918976129616
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