[gmx-users] Error message while running energy minimization

Deep Bhattacharya hypergenetics at gmail.com
Wed Jul 13 19:48:21 CEST 2016


Thanks. So I was looking at my ligand topology for the largest charged
group, it is the SDmso type of atom. This was generated using PRODRG
How can I fix this if this is the issue?

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1        OA     1  UNK     OHF     1   -0.723  15.9994
     2     SDmso     1  UNK     SHD     1    2.191  32.0600
     3        OM     1  UNK     OHE     1   -1.188  15.9994
 45        OA     1  UNK     OGF     8   -0.189  15.9994
    46     SDmso     1  UNK     SGG     8    2.191  32.0600
    47        OA     1  UNK     OGI     8   -0.722  15.9994

Please help

On Wed, Jul 13, 2016 at 12:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/13/16 1:19 PM, Deep Bhattacharya wrote:
>
>> I modified the em.mdp file
>>
>>
>> ; LINES STARTING WITH ';' ARE COMMENTS
>> title = Minimization ; Title of run
>>
>> ; Parameters describing what to do, when to stop and what to save
>> integrator = steep ; Algorithm (steep = steepest descent minimization)
>> emtol = 1000.0   ; Stop minimization when the maximum force < 10.0 kJ/mol
>> emstep      = 0.01      ; Energy step size
>> nsteps = 500000   ; Maximum number of (minimization) steps to perform
>> energygrps = Protein UNK ; Which energy group(s) to write to disk
>>
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> nstlist = 1    ; Frequency to update the neighbor list and long range
>> forces
>> ns_type = grid ; Method to determine neighbor list (simple, grid)
>> rlist = 1.4 ; Cut-off for making neighbor list (short range forces)
>> coulombtype = PME ; Treatment of long range electrostatic interactions
>> rcoulomb = 1.4 ; long range electrostatic cut-off
>> rvdw = 1.4 ; long range Van der Waals cut-off
>> pbc    = xyz ; Periodic Boundary Conditions (yes/no)
>> epsilon-rf     = 61
>>
>> When I try putting rcoulomb =0.8 as you had suggested, I get this error
>> message
>> ERROR 1 [file em.mdp]: With coulombtype = PME (without modifier), rcoulomb
>> must be equal to rlist, or rlistlong if nstcalclr=1. For optimal energy
>> conservation,consider using a potential modifier.
>> Do I need to use a potential modifier as it suggests?
>>
>>
> You need to set rlist = rcoulomb = rvdw as has already been stated.  Note
> that rcoulomb becomes somewhat flexible when using PME, so you don't
> necessarily *need* to stick to 0.8.
>
> -Justin
>
>
> On Wed, Jul 13, 2016 at 12:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 7/13/16 1:05 PM, Deep Bhattacharya wrote:
>>>
>>> I am using GROMACS v.4.6. Does using Verlet cut-off scheme lead to
>>>> problems
>>>> like blowing up of the system?
>>>>
>>>>
>>> No, you can't blame crashes on the Verlet algorithm.  It should be more
>>> accurate than anything else.  Systems typically crash because of (1)
>>> inadequate preparation/minimization, (2) bad topology, (3) inappropriate
>>> .mdp settings, or some combination thereof.
>>>
>>> When you say the largest charge in the topology you mean the combined
>>>
>>>> protein-ligand pdb?
>>>>
>>>>
>>> No, I mean the topology, not the coordinates.
>>>
>>> I have attached the .top and combined pdb file.
>>>
>>>>
>>>>
>>>> The list does not accept attachments, nor would any serve any purpose.
>>> You can easily inspect the topology with a simple text editor.
>>>
>>> -Justin
>>>
>>>
>>> Please help
>>>
>>>> Deep
>>>>
>>>> On Wed, Jul 13, 2016 at 11:56 AM, Justin Lemkul <jalemkul at vt.edu>
>>>> wrote:
>>>>
>>>>
>>>>
>>>>> On 7/13/16 12:25 PM, Deep Bhattacharya wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>>>
>>>>>> This is the error message that I am getting trying to run energy
>>>>>> minimization
>>>>>>
>>>>>>
>>>>>> It's not an error, it's a note.  That means, "for your information,
>>>>>> here
>>>>>>
>>>>> is something you may want to check."  It does not necessarily mean
>>>>> anything
>>>>> is wrong (that's what an "error" is).
>>>>>
>>>>> NOTE 2 [file topol.top]:
>>>>>
>>>>>   The largest charge group contains 11 atoms.
>>>>>>   Since atoms only see each other when the centers of geometry of the
>>>>>> charge
>>>>>>   groups they belong to are within the cut-off distance, too large
>>>>>> charge
>>>>>>   groups can lead to serious cut-off artifacts.
>>>>>>   For efficiency and accuracy, charge group should consist of a few
>>>>>> atoms.
>>>>>>   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO,
>>>>>> etc.
>>>>>>
>>>>>>
>>>>>> So look at your topology.  Where's your largest charge group?  If
>>>>>> you're
>>>>>>
>>>>> using the Verlet cutoff scheme, it's completely irrelevant. You don't
>>>>> specify a cutoff-scheme explicitly your .mdp but it is the default in
>>>>> recent versions, but you haven't said which GROMACS version you're
>>>>> using.
>>>>>
>>>>> -Justin
>>>>>
>>>>> em.mdp
>>>>>
>>>>>
>>>>>> ; minim.mdp - used as input into grompp to generate em.tpr
>>>>>> define       =  -DPOSRES -DPOSRES_LIGAND
>>>>>> integrator = steep
>>>>>> emtol = 1000.0
>>>>>> emstep      = 0.01
>>>>>> nsteps = 500000
>>>>>> energygrps              = System
>>>>>> nstlist    = 1
>>>>>> rlist               = 1.4
>>>>>> ns_type    = grid
>>>>>> coulombtype    = PME
>>>>>> rcoulomb    = 1.4
>>>>>> vdwtype        = cut-off
>>>>>> rvdw    = 1.4
>>>>>> pbc    = xyz
>>>>>> epsilon-rf     = 61
>>>>>>
>>>>>> Please help
>>>>>>
>>>>>> *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
>>>>>>
>>>>>>
>>>>>> --
>>>>>>
>>>>> ==================================================
>>>>>
>>>>> 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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
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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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
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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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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>
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-- 
Deep Bhattacharya.
Post-Graduate Student,
Department of Pharmaceutical Chemistry,
Bombay College Of Pharmacy.
Mobile - +918976129616


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