[gmx-users] Error message while running energy minimization
Deep Bhattacharya
hypergenetics at gmail.com
Wed Jul 13 20:30:08 CEST 2016
I am trying to use ATB to generate topologies by no entries for mass
values which is very suprising.
I had chopped out the rest as it was exceeding the size.
Would you suggest any other ligand topologies program?
[ moleculetype ]
; Name nrexcl
TX3M 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass total_charge
1 O 1 TX3M O104 261 %% 15.9994
2 C 1 TX3M C96 260 %% 12.0110
3 OA 1 TX3M O105 262 %% 15.9994
4 H 1 TX3M H48 263 %% 1.0080
5 C 1 TX3M C17 37 %% 12.0110
6 OE 1 TX3M O15 36 %% 15.9994
7 C 1 TX3M C16 35 %% 12.0110
8 OE 1 TX3M O18 42 %% 15.9994
9 C 1 TX3M C18 43 %% 12.0110
10 C 1 TX3M C22 48 %% 12.0110
11 NT 1 TX3M N7 257 %% 14.0067
12 H 1 TX3M H47 259 %% 1.0080
13 H 1 TX3M H46 258 %% 1.0080
14 C 1 TX3M C21 47 %% 12.0110
15 OE 1 TX3M O25 57 %% 15.9994
16 C 1 TX3M C24 58 %% 12.0110
17 C 1 TX3M C28 63 %% 12.0110
18 C 1 TX3M C95 253 %% 12.0110
On Wed, Jul 13, 2016 at 1:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/13/16 2:05 PM, Deep Bhattacharya wrote:
>
>> Can I use ATB topology for GROMOS53a6 forcefield?
>>
>>
> That's certainly a better source. Please refer to existing (and ongoing)
> threads regarding ATB, ligand topologies, etc.
>
> -Justin
>
>
> 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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>>>>>>>>> or
>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> --
>>>>>>>>
>>>>>>>> ==================================================
>>>>>>>
>>>>>>> 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
>>>>>
>>>>> * 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
>>>
>>> * Please search the archive at
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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
>
> * 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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