Re: [gmx-users] gmx conver-tpr error

[Amali Guruge]

Dear Dr. Justin,

Thank you very much for the reply.
I'm sure, I used -extend for the gmx convert-tpr.

How can I solve this problem?
Appreciate, if you could help me.
Thank you.


On Wed, May 30, 2018 at 9:51 PM, Justin Lemkul  wrote:

>
>
> On 5/30/18 5:51 AM, Amali Guruge wrote:
>
>> Dear Gromacs users,
>>
>> I did a simulation for a 50 ns and I want to extend it  by anther 50 ns.
>> Therefore, I used the command,
>> gmx convert-tpr -s run01.tpr -extend 5 -o run02.tpr
>> But I got the error, 'You've simulated long enough. Not writing tpr file.'
>>
>> How can I solve the problem?
>>
>
> Are you sure that was your exact command? You didn't accidentally type
> "-until" rather than "-extend" in your command? Any use of -extend
> shouldn't trigger that error, but -until would do exactly that in this
> instance.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
>
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[gmx-users] gmx conver-tpr error

[Amali Guruge]

Dear Gromacs users,

I did a simulation for a 50 ns and I want to extend it  by anther 50 ns.
Therefore, I used the command,
gmx convert-tpr -s run01.tpr -extend 5 -o run02.tpr
But I got the error, 'You've simulated long enough. Not writing tpr file.'

How can I solve the problem?

Thank you.




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[gmx-users] Solvation of the bilayer

[Amali Guruge]

Dear Gromacs users,

I have a bilayer in xy plane. I tried to solvate the bilayer
(sur_bilayer.pdb) with water molecules using gmx solvate. I used the
command;
gmx solvate -cp sur_bilayer.pdb -maxsol 28197 -o sur_water_bilayer.pdb

However, water molecules are not distributed in the hydrophilic layers in
the xy plane as I wanted. How can I solve this problem?


Thank you.




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Re: [gmx-users] Gromacs simulation with PEG

[Amali Guruge]

Dear Gromacs Users,

Thank you very much.

On Mon, Nov 13, 2017 at 9:56 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 11/12/17 5:51 PM, Amali Guruge wrote:
>
>> Dear Gromacs users,
>>
>> I tried to simulate a system which contains PEG and water. According to
>> the
>> phase diagram of PEG, it should form micells after the simulation.
>> However,
>> after the simulation PEG doesn't form micells. What could be the reason
>> for
>> this. Can anyone help me.
>>
>
> Any number of things, none of which you've described to us - insufficient
> simulation time, inadequate force field, mismatching conditions (i.e. not
> replicating experiment exactly), etc.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
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[gmx-users] Gromacs simulation with PEG

[Amali Guruge]

Dear Gromacs users,

I tried to simulate a system which contains PEG and water. According to the
phase diagram of PEG, it should form micells after the simulation. However,
after the simulation PEG doesn't form micells. What could be the reason for
this. Can anyone help me.

Thank you.
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Re: [gmx-users] Too many LINCS warnings when changed the time step

[Amali Guruge]

Dear Dr. Justin,

Thank you very much for the reply. If I keep the 0.005 as the time step,
what steps should be followed in-order to avoid the LINCS warnings?
Appreciate if you can comment on this.

Thank you.


On Thu, Nov 9, 2017 at 12:46 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 11/8/17 8:45 PM, Amali Guruge wrote:
>
>> Dear Gromacs users,
>>
>> I did energy minimization step and started the equilibration run. However,
>> when I changed the time step 0.002 to to 0.005, it gave an error; Too many
>> LINCS warnings. What could be the reason for this? The simulation was
>> worked without an error until I changed the time step. Appreciate if
>> anyone
>> can give me a solution.
>>
>
> A 5-fs timestep is only stable is using some topological modification like
> virtual sites and/or hydrogen mass repartitioning. Generally, a 2-fs
> timestep is an upper limit without such tricks.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
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[gmx-users] Too many LINCS warnings when changed the time step

[Amali Guruge]

Dear Gromacs users,

I did energy minimization step and started the equilibration run. However,
when I changed the time step 0.002 to to 0.005, it gave an error; Too many
LINCS warnings. What could be the reason for this? The simulation was
worked without an error until I changed the time step. Appreciate if anyone
can give me a solution.

Thank you.
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[gmx-users] tc-groups in mdp file

[Amali Guruge]

Dear gmx users,

My system contains ~ 700 polyethylene glycol (PEG) molecules and ~96000
water molecules (SOL). I would like to know that, do I have to use two
groups to control the temperature or just use one?

Can anyone help me?

Thank you.

Sincerely,
A. G. G
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[gmx-users] Water molecule can not be settled

[Amali Guruge]

Dear Gromacs users,

My system contains water molecules and polyethylene glycol molecules. I
generated the box (15.2*15.2*15.2 nm*3) using genbox command. Thereafter,
PEG molecules were added using gmx insert-molecules and solvated with gmx
solvate.

When I tried to run md, I got the following error.

step 1802: Water molecule starting at atom 93528 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)

my rum.mdp file contains following parameters.

integrator=  md
dt=  0.005
nsteps=  100
comm_mode=  linear
;
nstxout=  50
nstlog=  1000
nstenergy=  50
nstxtcout=  1
;
cutoff-scheme   =  Verlet
nstlist =  10
ns_type =  grid
pbc =  xyz
rlist   =  1.4
;
coulombtype =  PME
rcoulomb=  1.4
epsilon_r   =  1
rvdw=  1.4
fourierspacing  =  0.12
pme_order   =  4
ewald_rtol  =  1e-5
DispCorr=  EnerPres
;
Tcoupl=  v-rescale
tc-grps=  System
tau_t=  .1
ref_t=  298
;
Pcoupl=  parrinello-rahman
Pcoupltype=  isotropic
tau_p=  2.0
compressibility=  4.5e-5
ref_p=  1.0
;
gen_vel=  no
;
constraints=  all-bonds
constraint_algorithm=  lincs
lincs_order=  8


Can anyone help me to solve the error. The most of the people commented
previously that this error is due to a bad starting structure. If it is the
reason, how can I correct it.

Thank you.

Sincerely,
A Guruge
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Re: [gmx-users] Energy Minimization Error

[Amali Guruge]

Dear Gromacs users,

When I tried to run the equilibration run, it gave several LINCS WARNINGS.
However, that equilibration run is completed by the Gromacs. Do I have to
concern about these warnings or can I ignore those?

Thank you.

Sincerely,
A. Guruge

On Fri, Oct 20, 2017 at 11:22 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 10/19/17 8:21 PM, Amali Guruge wrote:
>
>> Dear Gromacs users,
>>
>> Thank you very much for the reply. My concern is "step 11: One or more
>> water molecules can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate". What
>> should I do to avoid it?
>>
>
> That happens often during minimization, especially the early steps. If it
> doesn't come back up again, it's fine. It should never happen during MD.
>
> -Justin
>
>
> Thank you.
>>
>> On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>> On 10/19/17 8:10 PM, Amali Guruge wrote:
>>>
>>> Dear Gromacs Users,
>>>>
>>>> I tried to energy minimize my system using the steep integrator.
>>>> However,
>>>> it gave the following message.
>>>>
>>>> Steepest Descents:
>>>>  Tolerance (Fmax)   =  5.0e+02
>>>>  Number of steps= 2000
>>>> Step=0, Dmax= 1.0e-02 nm, Epot=  3.96157e+06 Fmax= 1.00697e+06,
>>>> atom=
>>>> 14611
>>>> Step=1, Dmax= 1.0e-02 nm, Epot=  2.99970e+06 Fmax= 4.04778e+05,
>>>> atom=
>>>> 18527
>>>> Step=2, Dmax= 1.2e-02 nm, Epot=  1.54766e+06 Fmax= 1.52387e+05,
>>>> atom=
>>>> 1005
>>>> Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04,
>>>> atom=
>>>> 6994
>>>> Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04,
>>>> atom=
>>>> 58902
>>>> Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04,
>>>> atom=
>>>> 515
>>>> Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04,
>>>> atom=
>>>> 188631
>>>> Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04,
>>>> atom=
>>>> 188631
>>>> Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04,
>>>> atom=
>>>> 188631
>>>> Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04,
>>>> atom=
>>>> 188631
>>>> Step=   10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04,
>>>> atom=
>>>> 188631
>>>>
>>>> step 11: One or more water molecules can not be settled.
>>>> Check for bad contacts and/or reduce the timestep if appropriate.
>>>>
>>>> After 2000 steps it says,
>>>>
>>>> Steepest Descents did not converge to Fmax < 500 in 2001 steps.
>>>> Potential Energy  = -4.6310655e+06
>>>> Maximum force =  6.7453154e+03 on atom 18769
>>>> Norm of force =  3.3632809e+01
>>>>
>>>> Simulation ended prematurely, no performance report will be written.
>>>>
>>>>
>>>> my em.mdp file contains following parameters.
>>>>
>>>> integrator=  steep; simulation algorithm
>>>> dt=  0.002; time step (ps)
>>>> nsteps=  2000; # steps
>>>> comm_mode=  linear; c.o.m. motion reset
>>>> ;
>>>> ;Energy Minimization
>>>> emtol=  500; converged F lt value (kJ mol-1
>>>> nm-1)
>>>> emstep=  0.01 ; initial step size (nm)
>>>> ;
>>>> ;Output Control
>>>> nstxout=  5 ; write coordinates to .trr
>>>> nstvout=  5; write velocities to .trr
>>>> nstlog=  5; write energies to .log
>>>> nstenergy=  1; write energies to .edr
>>>> ;
>>>> ;Neightbour Searching
>>>> cutoff-scheme   =  Verlet; scheme used for
>>>> generating pair list
>>>> nstlist =  10   ; update neighbour list
>>>> ns_type=  grid; neighbour list method
>>>> pbc=  xyz; periodic boundary conditions
>>>> rlist=  0.9 ; cut-

Re: [gmx-users] Energy Minimization Error

[Amali Guruge]

Dear Gromacs users,

Thank you very much for the reply. My concern is "step 11: One or more
water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate". What
should I do to avoid it?

Thank you.

On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 10/19/17 8:10 PM, Amali Guruge wrote:
>
>> Dear Gromacs Users,
>>
>> I tried to energy minimize my system using the steep integrator. However,
>> it gave the following message.
>>
>> Steepest Descents:
>> Tolerance (Fmax)   =  5.0e+02
>> Number of steps= 2000
>> Step=0, Dmax= 1.0e-02 nm, Epot=  3.96157e+06 Fmax= 1.00697e+06, atom=
>> 14611
>> Step=1, Dmax= 1.0e-02 nm, Epot=  2.99970e+06 Fmax= 4.04778e+05, atom=
>> 18527
>> Step=2, Dmax= 1.2e-02 nm, Epot=  1.54766e+06 Fmax= 1.52387e+05, atom=
>> 1005
>> Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom=
>> 6994
>> Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom=
>> 58902
>> Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom=
>> 515
>> Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom=
>> 188631
>> Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom=
>> 188631
>> Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom=
>> 188631
>> Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom=
>> 188631
>> Step=   10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom=
>> 188631
>>
>> step 11: One or more water molecules can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>>
>> After 2000 steps it says,
>>
>> Steepest Descents did not converge to Fmax < 500 in 2001 steps.
>> Potential Energy  = -4.6310655e+06
>> Maximum force =  6.7453154e+03 on atom 18769
>> Norm of force =  3.3632809e+01
>>
>> Simulation ended prematurely, no performance report will be written.
>>
>>
>> my em.mdp file contains following parameters.
>>
>> integrator=  steep; simulation algorithm
>> dt=  0.002; time step (ps)
>> nsteps=  2000; # steps
>> comm_mode=  linear; c.o.m. motion reset
>> ;
>> ;Energy Minimization
>> emtol=  500; converged F lt value (kJ mol-1 nm-1)
>> emstep=  0.01 ; initial step size (nm)
>> ;
>> ;Output Control
>> nstxout=  5 ; write coordinates to .trr
>> nstvout=  5; write velocities to .trr
>> nstlog=  5; write energies to .log
>> nstenergy=  1; write energies to .edr
>> ;
>> ;Neightbour Searching
>> cutoff-scheme   =  Verlet; scheme used for
>> generating pair list
>> nstlist =  10   ; update neighbour list
>> ns_type=  grid; neighbour list method
>> pbc=  xyz; periodic boundary conditions
>> rlist=  0.9 ; cut-off for short-range neighbour
>> (nm)
>> ;
>> ;Electrostatics and VdW
>> coulombtype=  PME; type of coulomb interaction
>> rcoulomb=  0.9; cut-off distance for coulomb
>> epsilon_r=  1; dielectric constant
>> rvdw=  0.9; cut-off for vdw
>> fourierspacing=  0.12; maximum grid spacing for FFT
>> pme_order=  4; interpolation order for PME
>> ewald_rtol=  1e-5; relative strength of Ewald-shifted
>> DispCorr=  EnerPres ; long range dispersion
>> corrections
>> ;
>> ;Temperature Coupling
>> Tcoupl=  no; type of temperature coupling
>> ;
>> ;Pressure Coupling
>> Pcoupl=  no ; type of pressure coupling
>> ;
>> ;Velocity Generation
>> gen_vel=  no ; generate initial velocities
>> ;
>> ;Bonds
>> constraints=  none; bond constraint type
>>
>> I used gmx solvate to add water molecules to the system.
>>
>> How could I get rid of bad contacts of water molecules? Appreciate if
>> anyone help me to solve the problem.
>>
>
> mdrun stopped after 2000 steps because you told it to. Yo

[gmx-users] Energy Minimization Error

[Amali Guruge]

Dear Gromacs Users,

I tried to energy minimize my system using the steep integrator. However,
it gave the following message.

Steepest Descents:
   Tolerance (Fmax)   =  5.0e+02
   Number of steps= 2000
Step=0, Dmax= 1.0e-02 nm, Epot=  3.96157e+06 Fmax= 1.00697e+06, atom=
14611
Step=1, Dmax= 1.0e-02 nm, Epot=  2.99970e+06 Fmax= 4.04778e+05, atom=
18527
Step=2, Dmax= 1.2e-02 nm, Epot=  1.54766e+06 Fmax= 1.52387e+05, atom=
1005
Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom=
6994
Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom=
58902
Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom=
515
Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom=
188631
Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom=
188631
Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom=
188631
Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom=
188631
Step=   10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom=
188631

step 11: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

After 2000 steps it says,

Steepest Descents did not converge to Fmax < 500 in 2001 steps.
Potential Energy  = -4.6310655e+06
Maximum force =  6.7453154e+03 on atom 18769
Norm of force =  3.3632809e+01

Simulation ended prematurely, no performance report will be written.


my em.mdp file contains following parameters.

integrator=  steep; simulation algorithm
dt=  0.002; time step (ps)
nsteps=  2000; # steps
comm_mode=  linear; c.o.m. motion reset
;
;Energy Minimization
emtol=  500; converged F lt value (kJ mol-1 nm-1)
emstep=  0.01 ; initial step size (nm)
;
;Output Control
nstxout=  5 ; write coordinates to .trr
nstvout=  5; write velocities to .trr
nstlog=  5; write energies to .log
nstenergy=  1; write energies to .edr
;
;Neightbour Searching
cutoff-scheme   =  Verlet; scheme used for
generating pair list
nstlist =  10   ; update neighbour list
ns_type=  grid; neighbour list method
pbc=  xyz; periodic boundary conditions
rlist=  0.9 ; cut-off for short-range neighbour (nm)
;
;Electrostatics and VdW
coulombtype=  PME; type of coulomb interaction
rcoulomb=  0.9; cut-off distance for coulomb
epsilon_r=  1; dielectric constant
rvdw=  0.9; cut-off for vdw
fourierspacing=  0.12; maximum grid spacing for FFT
pme_order=  4; interpolation order for PME
ewald_rtol=  1e-5; relative strength of Ewald-shifted
DispCorr=  EnerPres ; long range dispersion
corrections
;
;Temperature Coupling
Tcoupl=  no; type of temperature coupling
;
;Pressure Coupling
Pcoupl=  no ; type of pressure coupling
;
;Velocity Generation
gen_vel=  no ; generate initial velocities
;
;Bonds
constraints=  none; bond constraint type

I used gmx solvate to add water molecules to the system.

How could I get rid of bad contacts of water molecules? Appreciate if
anyone help me to solve the problem.

Thank you.

Sincerely,
A Guruge
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[gmx-users] grompp error

[Amali Guruge]

Dear Gromacs users,

I got the following error when I tried to run grompp.
ERROR 1 [file system.top, line 18]:
  ERROR: One of the box lengths is smaller than twice the cut-off length.
  Increase the box size or decrease rlist

I increased the box size and re-tried to run grompp,but it didn't work. The
box size is 20*20*20 nm3. mdp file options are shown in below. Could you
please anyone help me to solve this problem.

Thank you.

; Define can be used to control processes
define  = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator= steep; Algorithm (steep = steepest descent
minimization)
emtol= 1.0; Stop minimization when the maximum force < 1.0
kJ/mol
nsteps= 200; Maximum number of (minimization) steps to
perform
nstenergy= 10; Write energies to disk every nstenergy steps
nstcalcenergy= 10; Calculate energy every step
energygrps= System; Which energy group(s) to write to disk
nstxout   = 100  ; Frequency of writing to .trr file


; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
cutoff-scheme   = Verlet
ns_type= simple; Method to determine neighbor list (simple,
grid)
coulombtype= cut-off; Treatment of long range electrostatic
interactions
rcoulomb= 1.0; long range electrostatic cut-off
rvdw= 1.0; long range Van der Waals cut-off
constraints= none; Bond types to replace by constraints
pbc= xyz; Periodic Boundary Conditions (yes/no)
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[gmx-users] Fwd: Simulation of surfactant and water composition

[Amali Guruge]

-- Forwarded message --
From: <gromacs.org_gmx-users-ow...@maillist.sys.kth.se>
Date: Thu, Oct 12, 2017 at 10:11 PM
Subject: Simulation of surfactant and water composition
To: amaligg2...@gmail.com


You are not allowed to post to this mailing list, and your message has
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-- Forwarded message --
From: Amali Guruge <amaligg2...@gmail.com>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Cc:
Bcc:
Date: Thu, 12 Oct 2017 22:11:11 +1100
Subject: Simulation of surfactant and water composition
Dear Gromacs users,

I want to model a system which contains surfactant molecules and water
molecules. I also want to model the system with w/w 15% surfactant/water
composition. Could you please guide me to model the system and do the
simulation using Gromacs software. Appreciate, if anyone can give a
tutorial to do the simulation in step by step.

Thank you.

Sincerely,
A Guruge
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Re: [gmx-users] Hbond occupancy

[Amali Guruge]

Thank you very much Eric for the answer. Could you please give information
regarding to the command use in this calculation? Thank you.

On Fri, Jul 8, 2016 at 5:31 PM, Erik Marklund <erik.markl...@chem.ox.ac.uk>
wrote:

> gmx hbond
>
> > On 8 Jul 2016, at 12:24, Amali Guruge <amaligg2...@gmail.com> wrote:
> >
> > Dear All,
> >
> > Can anyone know how to calculate H bond occupancy with Gromacs?
> >
> > Thank you
> > --
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[gmx-users] Hbond occupancy

[Amali Guruge]

Dear All,

Can anyone know how to calculate H bond occupancy with Gromacs?

Thank you
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[gmx-users] Residue Numbers

[Amali Guruge]

Dear All,

I used g_mmpbsa for free energy calculations. I competed contribution of
residues to the binding energy using python script. Original residue number
is available in final_contrib_energy.dat file. But we use energyMapIn.dat
file for the graph plotting. In that file residue numbers are different, it
always start with number one. How can I plot residue number vs energy
contribution? Can anyone help me?

Thank you.
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[gmx-users] Values for pcon & ncon in G_mmpbsa

[Amali Guruge]

Dear All,

In my MD simulation I only added counter ions (20 Na+ ions) to neutralize
the system. Now I want to do MM_PBSA calculations for my MD runs. In order
to do perform polar solvation energy, I have to define parameters pcon and
ncon.
According to my system what values should be assigned to those two
parameters? If I assign 0 (zero) value for both parameters, is it correct?

I don't have clear solution for this problem. Please can anyone help me?

Thank you in advance.
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[gmx-users] g_mmpbsa python script error

[Amali Guruge]

Dear All,


I installed g_mmpbsa tool for binding energy calculation for my GROMACS
runs. When I gave the command,

python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a sasa.xvg

I got the following error.

python: can't open file 'MmPbSaStat.py': [Errno 2] No such file or directory

Please can anyone help me to solve this problem.

Thank you.
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Re: [gmx-users] Number of H bonds formed between ligand and amino acid residues

[Amali Guruge]

Thank you very much for the answer. How we identify residues involving in H
bonds? In index file do we have to specify them?

On Tue, Jun 28, 2016 at 11:45 AM, Subhomoi Borkotoky <subhomoy...@gmail.com>
wrote:

> Hello,
>
> Please use the "hbond"  utility in gromacs.
>
> gmx hbond [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n
> [<.ndx>]][-num [<.xvg>]
>
>
> On Tue, Jun 28, 2016 at 11:24 AM, Amali Guruge <amaligg2...@gmail.com>
> wrote:
>
> > Dear Gromacs users,
> >
> > I carried out 20 ns long MD simulation for my receptor-ligand complex
> using
> > Gromacs software. Now I want to calculate number of hydrogen bonds formed
> > in the ligand and receptor corresponding to the residue number. Can
> anyone
> > help me?
> >
> >
> > Thank you.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Yours Sincerely,
> --
> SUBHOMOI BORKOTOKY,
> Centre for Bioinformatics
> Pondicherry University
> Pondicherry,INDIA.
>
> Alternate Email: subho...@mails.bicpu.edu.in
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[gmx-users] Number of H bonds formed between ligand and amino acid residues

[Amali Guruge]

Dear Gromacs users,

I carried out 20 ns long MD simulation for my receptor-ligand complex using
Gromacs software. Now I want to calculate number of hydrogen bonds formed
in the ligand and receptor corresponding to the residue number. Can anyone
help me?


Thank you.
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[gmx-users] MD Analysis

[Amali Guruge]

Dear Gromacs users,


I completed 20 ns MD simulation using GROMACS software. Now I want to
analyze the interactions were originally present and interactions were
created/lost during the simulation.  How can I do this? Can anyone help me?
Can I use AMBERTool for this? Please anyone recommend me a tutorial
regarding to this?

Thank you in advance.
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Re: [gmx-users] Getting pdb structure

[Amali Guruge]

Thank you all...

On Fri, Mar 25, 2016 at 7:52 PM, Erik Marklund <erik.markl...@chem.ox.ac.uk>
wrote:

>
> > On 25 Mar 2016, at 14:06, Erik Marklund <erik.markl...@chem.ox.ac.uk>
> wrote:
> >
> > gmx trjconv -f your.xc -s your.pr -o snapshot_at_8000.pdb -dump 8000
> >
>
> That should have been “-f your.xtc -s your.tpr”. I apologise on behalf of
> autocorrect.
>
> >> On 25 Mar 2016, at 13:30, Amali Guruge <amaligg2...@gmail.com> wrote:
> >>
> >> Dear All,
> >>
> >> I want to get the pdb structure of the system in 8000 ps time. The whole
> >> simulation contains 2 ps. How can I get the pdb structure of the
> system
> >> at that time?
> >> Can anyone help me?
> >>
> >> Thank you.
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
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> posting!
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[gmx-users] Getting pdb structure

[Amali Guruge]

Dear All,

I want to get the pdb structure of the system in 8000 ps time. The whole
simulation contains 2 ps. How can I get the pdb structure of the system
at that time?
Can anyone help me?

Thank you.
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[gmx-users] SwissParam and Gromacs

[Amali Guruge]

Dear All,

I submitted docked conformation of topotecan molecule to the SwissParam
server and I got itp file. Then I did a molecular dynamic simulation using
that itp file (I used Gromacs software with CHARMM27 force field)

When I tried to run the command,
 grompp -c b4em.pdb -f em01.mdp -n index.ndx -p system.top -o em01.tpr

it gave the following error.



*Fatal error:Atomtype CB not found*
I attached the itp file received from the server. Please help me to correct
this error.

Thank you.
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[gmx-users] Amber03 parameters for PTR

[Amali Guruge]

Dear All,

I want to do a molecular dynamic simulation for pdb ID 1K4T crystal
structure using Amber03 force field. The structure contains phosphotyrosine
(PTR). But parameters for PTR is not available in aminoacids.rtp file.
Therefore can anyone help me to solve my problem.

Thank you.
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Re: [gmx-users] Amber03 parameters for PTR

[Amali Guruge]

Dear Prof. Justin,

Thank you for the reply. Yes, I can use the parameters defined in that
site, but I have to define the aminoacids.hbd file as well for PTR. How can
I get that part?

Thank you.

On Wed, Oct 14, 2015 at 3:16 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 10/14/15 5:02 AM, Amali Guruge wrote:
>
>> Dear All,
>>
>> I want to do a molecular dynamic simulation for pdb ID 1K4T crystal
>> structure using Amber03 force field. The structure contains
>> phosphotyrosine
>> (PTR). But parameters for PTR is not available in aminoacids.rtp file.
>> Therefore can anyone help me to solve my problem.
>>
>>
> http://sites.pharmacy.manchester.ac.uk/bryce/amber
>
> -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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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[gmx-users] Atom OXT in PHE

[Amali Guruge]

Dear all,


When I give pdb2gmx command I got the following error.

Atom OXT in residue PHE 765 was not found in rtp entry PHE with 20 atoms
while sorting.

How can I fix this problem? Can anyone help me?

Thank you...
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[gmx-users] PTR is not found in residue topology database

[Amali Guruge]

Dear all,

My enzyme contains PTR (phosphotyrosine) molecule which connect to the DNA.
When I run the command pdb2gmx, it gives an error stating that PTR is not
found in residue topology database.

How can I fix this problem?
Can anyone help me?

Thank you.
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[gmx-users] MD with DNA double strand

[Amali Guruge]

Dear Gromacs users,

I want to do a molecular dynamic simulation for my enzyme-ligand complex.
The enzyme is topoisomerase I. I used the pdb id 1K4T for the simulation
and I need to keep the DNA double strand with the enzyme.

I replaced the 5'-sulfhydryl group into a 5'-hydroxyl group before starting
the simulation.

I gave the command 'pdb2gmx -f receptor.pdb -inter -p system.top -o
recep01.pdb -ignh'. I selected AMBER99 as the force field while SPC/E was
used as the water model.
Then I got the following error.

Fatal error:
Atom O in residue DG 11 was not found in rtp entry DG with 33 atoms
while sorting atoms.

How can I solve this problem? Can anyone help me?

Thank you.
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