[gmx-users] multiple ligands topology
Justin Lemkul
jalemkul at vt.edu
Fri Feb 13 16:01:34 CET 2015
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
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