[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
>>>
>>> ==================================================
>>> --
>>> 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
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> 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
>
> * 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
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list