[gmx-users] multiple ligands topology

Justin Lemkul jalemkul at vt.edu
Fri Feb 13 22:46:11 CET 2015



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/
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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
>>
>> * For (un)subscribe requests visit
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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

==================================================


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