[gmx-users] Error message while running energy minimization
Deep Bhattacharya
deep.bhattacharya1991 at gmail.com
Wed Jul 13 20:20:46 CEST 2016
I am trying to use ATB to generate topologies by no entries for mass
values?
I had chopped out the rest as it was exceeding the size.
Would you suggest any other ligand topologies program?
*Deep S Bhattacharya*
Graduate Research Assistant,
Department of Pharmaceutical sciences,
University of Nebraska Medical Center
Cell: (402) 906-8422
Work: (402) 559-4349
Email: deep.bhattacharya at unmc.edu, deep.bhattacharya1991 at gmail.com
*"Knowledge is power. Information is liberating. Education is the premise
of progress, in every society, in every family."*
*- Kofi Annan*
On Wed, Jul 13, 2016 at 1:05 PM, Deep Bhattacharya <hypergenetics at gmail.com>
wrote:
> 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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> >>> 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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> > posting!
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> >
>
>
>
> --
> Deep Bhattacharya.
> Post-Graduate Student,
> Department of Pharmaceutical Chemistry,
> Bombay College Of Pharmacy.
> Mobile - +918976129616
> --
> Gromacs Users mailing list
>
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