[gmx-users] multiple ligands topology
Jennifer Vo
quyviolet at gmail.com
Fri Feb 13 15:59:34 CET 2015
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.
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?
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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