[gmx-users] multiple ligands topology

Jennifer Vo quyviolet at gmail.com
Fri Feb 13 20:47:54 CET 2015


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)

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
### redefine the box the the system
editconf -f AB_NADPH_IR3.pdb -o AB_NADPH_IR3_box.pdb -bt cubic -d 1.0 -c
### 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
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
>>>
>>> ==================================================
>>> --
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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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