[gmx-users] multiple ligands topology
Jennifer Vo
quyviolet at gmail.com
Mon Feb 16 09:49:47 CET 2015
Dear Justin,
Many thanks again. I just define a small box then insert molecules and let
it floating nearby the protein, then redefine the actual box for the real
concentration of protein.
The maxwarn 27 is from this
"NOTE 1 [file em_ion.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to 2002995045
WARNING 1 [file my_ligand_atomtypes.itp, line 3]:
Overriding atomtype CA
WARNING 2 [file my_ligand_atomtypes.itp, line 4]:
Overriding atomtype H4
WARNING 3 [file my_ligand_atomtypes.itp, line 5]:
Overriding atomtype HA
WARNING 4 [file my_ligand_atomtypes.itp, line 6]:
Overriding atomtype C
WARNING 5 [file my_ligand_atomtypes.itp, line 7]:
Overriding atomtype O
WARNING 6 [file my_ligand_atomtypes.itp, line 8]:
Overriding atomtype N
WARNING 7 [file my_ligand_atomtypes.itp, line 9]:
Overriding atomtype H
WARNING 8 [file my_ligand_atomtypes.itp, line 10]:
Overriding atomtype N*
WARNING 9 [file my_ligand_atomtypes.itp, line 11]:
Overriding atomtype CT
WARNING 10 [file my_ligand_atomtypes.itp, line 12]:
Overriding atomtype H2
WARNING 11 [file my_ligand_atomtypes.itp, line 13]:
Overriding atomtype H1
WARNING 12 [file my_ligand_atomtypes.itp, line 14]:
Overriding atomtype OH
WARNING 13 [file my_ligand_atomtypes.itp, line 15]:
Overriding atomtype HO
WARNING 14 [file my_ligand_atomtypes.itp, line 16]:
Overriding atomtype OS
WARNING 15 [file my_ligand_atomtypes.itp, line 17]:
Overriding atomtype P
WARNING 16 [file my_ligand_atomtypes.itp, line 18]:
Overriding atomtype O2
WARNING 17 [file my_ligand_atomtypes.itp, line 19]:
Overriding atomtype CK
WARNING 18 [file my_ligand_atomtypes.itp, line 20]:
Overriding atomtype H5
WARNING 19 [file my_ligand_atomtypes.itp, line 21]:
Overriding atomtype NB
WARNING 20 [file my_ligand_atomtypes.itp, line 22]:
Overriding atomtype CB
WARNING 21 [file my_ligand_atomtypes.itp, line 23]:
Overriding atomtype N2
WARNING 22 [file my_ligand_atomtypes.itp, line 24]:
Overriding atomtype NC
WARNING 23 [file my_ligand_atomtypes.itp, line 25]:
Overriding atomtype CQ
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'A'
Excluding 3 bonded neighbours molecule type 'B'
Excluding 3 bonded neighbours molecule type 'NPD'
Excluding 3 bonded neighbours molecule type 'IR3'
Excluding 2 bonded neighbours molecule type 'SOL'
"
And I think it's harmless to ignore the warning here for the overriding
atomtype. Am I correct? The image of ligand is in the link
http://postimg.org/image/fojbmkhrb/
I would really appreciate for a help.
Regards,
Jennifer
On Fri, Feb 13, 2015 at 10:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 2/13/15 2:47 PM, Jennifer Vo wrote:
>
>> Dear Justin,
>> Please find the figure of output pdb file after minimizatrion.(I have sent
>> in the previous email but it's pending... So I send it again)
>>
>>
> The list doesn't accept attachments (if I had a nickel for every time I
> said that...) so if you want to share images, upload them to a file-sharing
> service and post the URL.
>
> Here is step by step how I built the system
>> ### concatenate 2 chains and renumber the residues
>> genconf -f AB.gro -o AB_renumber.gro -renumber
>> ### redefine the small box the the proteins
>> editconf -f AB_renumber.gro -o AB_box.gro -bt cubic -d 0.5 -c
>> ### insert the first ligand
>> gmx insert-molecules -f AB_box.gro -ci ligand1.gro -o AB_NADPH.pdb
>> -nmol 1
>> ### insert the second ligand
>> gmx insert-molecules -f AB_NADPH.pdb -ci ir3_em.gro -o AB_NADPH_IR3.pdb
>> -nmol 9 -seed -1
>>
>
> OK, so "ligands" are actually just randomly inserted molecules, freely
> floating in the solvent.
>
> ### redefine the box the the system
>> editconf -f AB_NADPH_IR3.pdb -o AB_NADPH_IR3_box.pdb -bt cubic -d 1.0 -c
>>
>
> Why is this necessary?
>
> ### adding water
>> gmx solvate -cp AB_NADPH_IR3_box.pdb -cs spc216.gro -o
>> AB_NADPH_IR3_solvate.pdb -p topol.top
>> ### convert pdb to gro file
>> editconf -f AB_NADPH_IR3_solvate.pdb -o AB_NADPH_IR3_solvate.gro
>> ### adding ions
>> grompp -f em_ion.mdp -c AB_NADPH_IR3_solvate.gro -p topol.top -o ions.tpr
>> -maxwarn 27
>>
>
> The use of -maxwarn 27 is alarming. Why are you trying to override 27
> errors? This would be suspect #1 in diagnosing problems.
>
> -Justin
>
>
> genion -s ions.tpr -o AB_NADPH_IR3_solvate_ions.gro -p topol.top -pname NA
>> -np 24 -n index.ndx
>>
>> Many thanks for your help.
>>
>> On Fri, Feb 13, 2015 at 4:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 2/13/15 9:59 AM, Jennifer Vo wrote:
>>>
>>> Dear Justin,
>>>> Many thanks for your kind answer. The output of minimization for
>>>> Protein +
>>>> 1 Ligand
>>>> Steepest Descents converged to Fmax < 100 in 868 steps
>>>> Potential Energy = -8.0409740e+06
>>>> Maximum force = 8.3073639e+01 on atom 267747
>>>> Norm of force = 3.5544858e+00
>>>>
>>>> The out for Protein + 2 ligands
>>>> Steepest Descents converged to Fmax < 100 in 2165 steps
>>>> Potential Energy = -6.2125650e+06
>>>> Maximum force = 8.6047729e+01 on atom 263858
>>>> Norm of force = 3.6529241e+00
>>>>
>>>> I don't see any failure. But when I use trjconv from Output gro file to
>>>> pdb
>>>> file, I see the ligands screwed up.
>>>>
>>>>
>>> Again, please define what this means. How did you build the system? Can
>>> you share an image?
>>>
>>> In case "The ligand files are both set up within different boxes, so
>>>
>>>> perhaps the construction of your system is incorrect somehow", how do I
>>>> fix
>>>> it? Do I have to change the final line of every ligand's topology file?
>>>>
>>>>
>>> Well, assuming you're copying and pasting coordinates to construct the
>>> system, if they're defined in different boxes, they're probably not going
>>> to be where they should be when you define a third box with different
>>> dimensions, unless you're using editconf to reposition in between.
>>> Again,
>>> you'll need to provide actual specifics of how you built the system
>>> (step-by-step commands, please).
>>>
>>> -Justin
>>>
>>>
>>> Which are
>>>
>>>>
>>>> 1IR3 HAF 22 10.581 10.138 10.385
>>>> 20.72517 20.72517 20.72517
>>>> and
>>>> 1NPD H8A 73 -0.376 0.292 -5.440
>>>> 1.94588 0.88647 1.08377
>>>>
>>>> and the box of the System including Proteins + 2 ligands
>>>>
>>>> 23746NA NA79296 15.582 10.741 1.636
>>>> 15.63000 15.63000 15.63000
>>>>
>>>> Many thanks in advance!
>>>> Jennifer
>>>>
>>>>
>>>> On Fri, Feb 13, 2015 at 3:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>>> On 2/13/15 6:03 AM, Jennifer Vo wrote:
>>>>>
>>>>> Dear All,
>>>>>
>>>>>> I am running a simulation for a systems including two chains of
>>>>>> proteins
>>>>>> and two ligands using amber 99SB ff.
>>>>>> My topol.top is
>>>>>>
>>>>>> #include "amber99sb.ff/forcefield.itp"
>>>>>> #include "my_ligand_atomtypes.itp"
>>>>>>
>>>>>> ; Include chain topologies
>>>>>> #include "A.itp"
>>>>>> #ifdef POSRES
>>>>>> #include "posre_A.itp"
>>>>>> #endif
>>>>>> #include "B.itp"
>>>>>> #ifdef POSRES
>>>>>> #include "posre_B.itp"
>>>>>> #endif
>>>>>>
>>>>>> ; Include custom ligand topologies
>>>>>> #include "npd.itp"
>>>>>> #ifdef POSRES_LIG
>>>>>> #include "posre_npd.itp"
>>>>>> #endif
>>>>>> ; Include custom ligand topologies
>>>>>> #include "ir3_em.itp"
>>>>>> ; Include water topology
>>>>>> #include "amber99sb.ff/tip3p.itp"
>>>>>>
>>>>>> #ifdef POSRES_WATER
>>>>>> ; Position restraint for each water oxygen
>>>>>> [ position_restraints ]
>>>>>> ; i funct fcx fcy fcz
>>>>>> 1 1 1000 1000 1000
>>>>>> #endif
>>>>>> ; Include generic ion topology
>>>>>> #include "amber99sb.ff/ions.itp"
>>>>>>
>>>>>> [ system ]
>>>>>> ; Name
>>>>>> BcSIRED in water
>>>>>> [ molecules ]
>>>>>> ; Compound #mols
>>>>>> A 1
>>>>>> B 1
>>>>>> NPD 1
>>>>>> IR3 9
>>>>>> SOL 123406
>>>>>> NA 24
>>>>>>
>>>>>> then I have my_ligand_atomtypes.itp
>>>>>> [ atomtypes ]
>>>>>> ;name bond_type mass charge ptype sigma epsilon
>>>>>> Amb
>>>>>> CA CA 0.00000 0.00000 A 3.39967e-01
>>>>>> 3.59824e-01
>>>>>> ;
>>>>>> 1.91 0.0860
>>>>>> H4 H4 0.00000 0.00000 A 2.51055e-01
>>>>>> 6.27600e-02
>>>>>> ;
>>>>>> 1.41 0.0150
>>>>>> HA HA 0.00000 0.00000 A 2.59964e-01
>>>>>> 6.27600e-02
>>>>>> ;
>>>>>> 1.46 0.0150
>>>>>> C C 0.00000 0.00000 A 3.39967e-01
>>>>>> 3.59824e-01
>>>>>> ;
>>>>>> 1.91 0.0860
>>>>>> O O 0.00000 0.00000 A 2.95992e-01
>>>>>> 8.78640e-01
>>>>>> ;
>>>>>> 1.66 0.2100
>>>>>> N N 0.00000 0.00000 A 3.25000e-01
>>>>>> 7.11280e-01
>>>>>> ;
>>>>>> 1.82 0.1700
>>>>>> H H 0.00000 0.00000 A 1.06908e-01
>>>>>> 6.56888e-02
>>>>>> ;
>>>>>> 0.60 0.0157
>>>>>> N* N* 0.00000 0.00000 A 3.25000e-01
>>>>>> 7.11280e-01
>>>>>> ;
>>>>>> 1.82 0.1700
>>>>>> CT CT 0.00000 0.00000 A 3.39967e-01
>>>>>> 4.57730e-01
>>>>>> ;
>>>>>> 1.91 0.1094
>>>>>> H2 H2 0.00000 0.00000 A 2.29317e-01
>>>>>> 6.56888e-02
>>>>>> ;
>>>>>> 1.29 0.0157
>>>>>> H1 H1 0.00000 0.00000 A 2.47135e-01
>>>>>> 6.56888e-02
>>>>>> ;
>>>>>> 1.39 0.0157
>>>>>> OH OH 0.00000 0.00000 A 3.06647e-01
>>>>>> 8.80314e-01
>>>>>> ;
>>>>>> 1.72 0.2104
>>>>>> HO HO 0.00000 0.00000 A 0.00000e+00
>>>>>> 0.00000e+00
>>>>>> ;
>>>>>> 0.00 0.0000
>>>>>> OS OS 0.00000 0.00000 A 3.00001e-01
>>>>>> 7.11280e-01
>>>>>> ;
>>>>>> 1.68 0.1700
>>>>>> P P 0.00000 0.00000 A 3.74177e-01
>>>>>> 8.36800e-01
>>>>>> ;
>>>>>> 2.10 0.2000
>>>>>> O2 O2 0.00000 0.00000 A 2.95992e-01
>>>>>> 8.78640e-01
>>>>>> ;
>>>>>> 1.66 0.2100
>>>>>> CK CK 0.00000 0.00000 A 3.39967e-01
>>>>>> 3.59824e-01
>>>>>> ;
>>>>>> 1.91 0.0860
>>>>>> H5 H5 0.00000 0.00000 A 2.42146e-01
>>>>>> 6.27600e-02
>>>>>> ;
>>>>>> 1.36 0.0150
>>>>>> NB NB 0.00000 0.00000 A 3.25000e-01
>>>>>> 7.11280e-01
>>>>>> ;
>>>>>> 1.82 0.1700
>>>>>> CB CB 0.00000 0.00000 A 3.39967e-01
>>>>>> 3.59824e-01
>>>>>> ;
>>>>>> 1.91 0.0860
>>>>>> N2 N2 0.00000 0.00000 A 3.25000e-01
>>>>>> 7.11280e-01
>>>>>> ;
>>>>>> 1.82 0.1700
>>>>>> NC NC 0.00000 0.00000 A 3.25000e-01
>>>>>> 7.11280e-01
>>>>>> ;
>>>>>> 1.82 0.1700
>>>>>> CQ CQ 0.00000 0.00000 A 3.39967e-01
>>>>>> 3.59824e-01
>>>>>> ;
>>>>>> 1.91 0.0860
>>>>>> ; IR3_GMX.top created by acpype (Rev: 403) on Wed Feb 4 11:55:46
>>>>>> 2015
>>>>>> ; Include forcefield parameters
>>>>>> [ atomtypes ]
>>>>>> ;name bond_type mass charge ptype sigma
>>>>>> epsilon Amb
>>>>>> C C 0.00000 0.00000 A 3.39967e-01
>>>>>> 3.59824e-01
>>>>>> ;
>>>>>> 1.91 0.0860
>>>>>> H H 0.00000 0.00000 A 1.06908e-01
>>>>>> 6.56888e-02
>>>>>> ;
>>>>>> 0.60 0.0157
>>>>>> N N 0.00000 0.00000 A 3.25000e-01
>>>>>> 7.11280e-01
>>>>>> ;
>>>>>> 1.82 0.1700
>>>>>>
>>>>>> My first ligand gro file
>>>>>> GRoups of Organic Molecules in ACtion for Science
>>>>>> 73
>>>>>> 1NPD OA22 1 -0.282 0.251 -5.719
>>>>>> 1NPD OA23 2 -0.142 0.366 -5.542
>>>>>> 1NPD OA24 3 -0.039 0.314 -5.771
>>>>>> 1NPD P'A2 4 -0.145 0.285 -5.669
>>>>>> 1NPD PA 5 -0.033 -0.056 -5.010
>>>>>> 1NPD PN 6 -0.130 -0.245 -4.804
>>>>>> 1NPD O3P 7 -0.126 -0.116 -4.893
>>>>>> 1NPD N1A 8 -0.692 0.110 -5.840
>>>>>> 1NPD N1N 9 -0.539 -0.355 -4.443
>>>>>> 1NPD C2A 10 -0.613 0.000 -5.836
>>>>>> ...
>>>>>> 1NPD H8A 73 -0.376 0.292 -5.440
>>>>>> 1.94588 0.88647 1.08377
>>>>>>
>>>>>> My second ligand gro file
>>>>>>
>>>>>> IR3_GMX.gro created by acpype (Rev: 403) on Wed Feb 4 11:55:46 2015
>>>>>> 22
>>>>>> 1IR3 CAA 1 10.182 10.576 10.387
>>>>>> 1IR3 HAB 2 10.211 10.640 10.305
>>>>>> 1IR3 HAA 3 10.075 10.577 10.396
>>>>>> ....
>>>>>> 1IR3 HAF 22 10.581 10.138 10.385
>>>>>> 20.72517 20.72517 20.72517
>>>>>>
>>>>>> but the system can`t go under energy minimization. This is my em.mdp
>>>>>>
>>>>>> title = Minimization ; Title of run
>>>>>> integrator = steep ; Algorithm (steep = steepest descent
>>>>>> minimization)
>>>>>> emtol = 1000.0 ; Stop minimization when the maximum
>>>>>> force
>>>>>> < 1000.0 kJ/mol
>>>>>> emstep = 0.01 ; Energy step size
>>>>>> nsteps = 500000 ; Maximum number of
>>>>>> (minimization)
>>>>>> steps to perform
>>>>>> energygrps = Protein NPD IR3 ; Which energy group(s) to
>>>>>> write
>>>>>> to
>>>>>> disk
>>>>>> nstlist = 1 ; Frequency to update the neighbor
>>>>>> list
>>>>>> and long range forces
>>>>>> cutoff-scheme = Verlet
>>>>>> 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
>>>>>>
>>>>>> I change emtol from 1000, then 500, then 100. No error generated but
>>>>>> the
>>>>>> pdb output file goes wrong with the ligands. If I do the same
>>>>>> procedure
>>>>>> with seperated ligand (only one [ atomtypes] in
>>>>>> my_ligand_atomtypes.itp),
>>>>>> things goes well . Could you please help me where is the problem?
>>>>>> Many thanks in advance.
>>>>>>
>>>>>>
>>>>>> You'll have to be much more specific than "goes wrong with the
>>>>> ligands."
>>>>> What's happening? Does EM fail or is the output just somehow screwed
>>>>> up?
>>>>> The ligand files are both set up within different boxes, so perhaps the
>>>>> construction of your system is incorrect somehow, but again, without
>>>>> specifics, I'm just guessing.
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> 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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>>>>>
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>>>>> 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
>>>
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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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