[gmx-users] Error message while running energy minimization
Deep Bhattacharya
hypergenetics at gmail.com
Wed Jul 13 20:05:35 CEST 2016
Can I use ATB topology for GROMOS53a6 forcefield?
Deep
On Wed, Jul 13, 2016 at 12:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/13/16 1:48 PM, Deep Bhattacharya wrote:
>
>> 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
>>
>>
> Each of those charge groups has three atoms (unless you've chopped out the
> rest of each), so no, that is not the problem grompp is complaining about.
> Again, with the Verlet cutoff scheme, the message is completely irrelevant.
>
> In general, don't use PRODRG topologies that have not been carefully
> refined. They are of poor quality and this is likely a contributor to your
> instability.
>
>
> -Justin
>
> 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
>>>>>>>
>>>>>>> * Please search the archive at
>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>> posting!
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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
>>>
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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
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>
--
Deep Bhattacharya.
Post-Graduate Student,
Department of Pharmaceutical Chemistry,
Bombay College Of Pharmacy.
Mobile - +918976129616
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