[gmx-users] MD simulation error

[Anjana Jayasinghe]

Dear Gromacs users,

If I am not getting the expecting (experimental) behavoir of my system using MD 
simulations, what could be the best option to do with MD simulations?

Thank you.
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Re: [gmx-users] MD simulation error : rRNA simulaion

[Tasneem Kausar]

In energy group you have given Potein and non-Protein and you are not
simulation a protein but RNA.

On Fri, Oct 6, 2017 at 12:53 AM, Hemant Arya 
wrote:

> Dear gromacs,
> Greetings
> I am trying to run a NVT with the following command.
>
> My mdp file is below
>
> title   = Protein-ligand complex NVT equilibration
> define  = -DPOSRES  ; position restrain the protein and ligand
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 5 ; 2 * 5 = 100 ps
> dt  = 0.002 ; 2 fs
> ; Output control
> nstxout = 500   ; save coordinates every 0.2 ps
> nstvout = 500   ; save velocities every 0.2 ps
> nstenergy   = 500   ; save energies every 0.2 ps
> nstlog  = 500   ; update log file every 0.2 ps
> energygrps  = Protein Non-protein
> ; Bond parameters
> continuation= no; first dynamics run
> constraint_algorithm = lincs; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> cutoff-scheme   = Verlet
> ns_type = grid  ; search neighboring grid cells
> nstlist = 10 ; 10 fs
> *rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)*
> *rvdw= 1.4   ; short-range van der Waals cutoff (in nm)*
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.16  ; grid spacing for FFT
> ; Temperature coupling
> tcoupl  = V-rescale ; modified Berendsen thermostat
> tc_grps = Protein Non-Protein; two coupling groups - more accurate
> tau_t   = 0.1   0.1 ; time constant, in ps
> ref_t   = 300   300 ; reference temperature, one
> for each group, in K
> ; Pressure coupling
> pcoupl  = no; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc = xyz   ; 3-D PBC
> ; Dispersion correction
> DispCorr= EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = yes   ; assign velocities from Maxwell distribution
> gen_temp= 300   ; temperature for Maxwell distribution
> gen_seed= -1; generate a random seed
>
>
>
> Error :
>
> GROMACS:  gmx grompp, VERSION 5.1.4
> Executable:   /home/amouda/Desktop/gromacs-5.1.4/build/bin/gmx
> Data prefix:  /home/amouda/Desktop/gromacs-5.1.4 (source tree)
> Command line:
>   gmx grompp -f nvt.mdp -c em-steep.gro -p trp.top -o pr-nvt.tpr -n
> index.ndx
>
> Ignoring obsolete mdp entry 'title'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.17#
>
> *ERROR 1 [file nvt.mdp]:*
> *  With Verlet lists rcoulomb!=rvdw is not supported*
>
> Setting the LD random seed to 2859163501
> Generated 20503 of the 20503 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 17396 of the 20503 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'RNA_chain_1'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'NA'
> turning all bonds into constraints...
> Setting gen_seed to 1604041440
> Velocities were taken from a Maxwell distribution at 300 K
> Removing all charge groups because cutoff-scheme=Verlet
>
>
> When i gave equal parameter to coulomb (1.4) and rvdw (1.4) then it shows
> different error
> like
> "Fatal error:
> Group Protein referenced in the .mdp file was not found in the index file.
> Group names must match either [moleculetype] names or custom index group
> names, in which case you must supply an index file to the '-n' option
> of grompp."
>
>
> Please help me to solve the problem.
> Thanks
> --
> *Hemant Arya*
> Research Scholar
> UGC-RGNF
> Centre for Bioinformatics,
> School of Life Sciences,
> Pondicherry University
> Kalapet
> Puducherry- 605014
> INDIA
> Contact No. +91 9597221248
>+91 2930-244141
> --
> 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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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] MD simulation error : rRNA simulaion

[Hemant Arya]

Dear gromacs,
Greetings
I am trying to run a NVT with the following command.

My mdp file is below

title   = Protein-ligand complex NVT equilibration
define  = -DPOSRES  ; position restrain the protein and ligand
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 500   ; save coordinates every 0.2 ps
nstvout = 500   ; save velocities every 0.2 ps
nstenergy   = 500   ; save energies every 0.2 ps
nstlog  = 500   ; update log file every 0.2 ps
energygrps  = Protein Non-protein
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type = grid  ; search neighboring grid cells
nstlist = 10 ; 10 fs
*rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)*
*rvdw= 1.4   ; short-range van der Waals cutoff (in nm)*
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling
tcoupl  = V-rescale ; modified Berendsen thermostat
tc_grps = Protein Non-Protein; two coupling groups - more accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 300   300 ; reference temperature, one
for each group, in K
; Pressure coupling
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed



Error :

GROMACS:  gmx grompp, VERSION 5.1.4
Executable:   /home/amouda/Desktop/gromacs-5.1.4/build/bin/gmx
Data prefix:  /home/amouda/Desktop/gromacs-5.1.4 (source tree)
Command line:
  gmx grompp -f nvt.mdp -c em-steep.gro -p trp.top -o pr-nvt.tpr -n
index.ndx

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.17#

*ERROR 1 [file nvt.mdp]:*
*  With Verlet lists rcoulomb!=rvdw is not supported*

Setting the LD random seed to 2859163501
Generated 20503 of the 20503 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 17396 of the 20503 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'RNA_chain_1'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...
Setting gen_seed to 1604041440
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet


When i gave equal parameter to coulomb (1.4) and rvdw (1.4) then it shows
different error
like
"Fatal error:
Group Protein referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp."


Please help me to solve the problem.
Thanks
-- 
*Hemant Arya*
Research Scholar
UGC-RGNF
Centre for Bioinformatics,
School of Life Sciences,
Pondicherry University
Kalapet
Puducherry- 605014
INDIA
Contact No. +91 9597221248
   +91 2930-244141
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Re: [gmx-users] Md simulation error

[Justin Lemkul]

On 11/8/16 2:07 PM, maria khan wrote:

Dear justin lemkul,,
Thanks alot..i like the way u answer my stupid questions..actually i dont
have anyone to guide me except u.thats why i ask even stupid questions.dont
mind please.i want to work under your supervision because i have passion
for simulation on gromacs.
Now coming to the point,,my problem was concerned with his residue of atom
HD1.I just went to pdb file and rename that HD1 to H3.then two files formed
that are  " "posre _protein chain_A.itp  and  topol_protein_chain _A.itp""
.while  topol.top   remained empty.now it gives me another error that is
" " Residue 'IS A' not found in residue topology database"".


http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

-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] Md simulation error

[maria khan]

Dear justin lemkul,,
Thanks alot..i like the way u answer my stupid questions..actually i dont
have anyone to guide me except u.thats why i ask even stupid questions.dont
mind please.i want to work under your supervision because i have passion
for simulation on gromacs.
Now coming to the point,,my problem was concerned with his residue of atom
HD1.I just went to pdb file and rename that HD1 to H3.then two files formed
that are  " "posre _protein chain_A.itp  and  topol_protein_chain _A.itp""
.while  topol.top   remained empty.now it gives me another error that is
" " Residue 'IS A' not found in residue topology database"".
im using version 5.1.2 actually.
i 'll encourage and wellcome even live discussion with you.I studied your
papers on simulation.
Regards.
GOD bless you.
Maria khan
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[gmx-users] Md simulation error..

[maria khan]

Dear Justin A. Lemkul, than you so much..i Will follow that link you hv
provided..i will concern you for further progress.
regards.
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Re: [gmx-users] Md simulation error.

[Justin Lemkul]

On 10/30/16 4:41 PM, maria khan wrote:

Dear Justin A. Lemkul,,im very much thankful for your honourable response.
As i mentioned you that im beginner to use of gromacs,,can you send me all
these suggestions in the form of videos,because im not getting you and im
confuse.i have followed the manuals of gromacs bt i didnt understand it
properly and my background for simulation is not as such strong yet.
is there any tuitorials or online course on simulation of proteins and
ligand.?


http://www.gromacs.org/Documentation/Tutorials

-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] Md simulation error.

[maria khan]

Dear Justin A. Lemkul,,im very much thankful for your honourable response.
As i mentioned you that im beginner to use of gromacs,,can you send me all
these suggestions in the form of videos,because im not getting you and im
confuse.i have followed the manuals of gromacs bt i didnt understand it
properly and my background for simulation is not as such strong yet.
is there any tuitorials or online course on simulation of proteins and
ligand.?
regards..
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Re: [gmx-users] Md simulation error

[Justin Lemkul]

On 10/29/16 5:04 AM, maria khan wrote:

Thanks  alot  Justin A. Lemkulfor your strong concern.
can you please guide me in conforming protonation states for residues.im
new user of gromacs for simulation.


Start with some basic tutorials that show you how everything works in good 
systems.

Then consult the manual about what the force field files contain and what they 
do, particularly the .rtp files, which define required residue nomenclature. 
Then you will see how your file does not conform to what the force field 
requires.  Of course, the simplest solution is to do what pdb2gmx says and use 
-ignh to have the H atoms rebuilt with the proper names.  Many programs and 
structural databases do not conform to standard nomenclature, which prevents 
pdb2gmx (or any topology-generating software, it's not like this is just a 
GROMACS problem) from working properly.


-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] Md simulation error

[maria khan]

Thanks  alot  Justin A. Lemkulfor your strong concern.
can you please guide me in conforming protonation states for residues.im
new user of gromacs for simulation.
Regards.
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Re: [gmx-users] Md simulation error

[Justin Lemkul]

On 10/27/16 2:03 PM, maria khan wrote:

Hello dear gromacs users,
i m running md simulation for protein ligand complex that are glutamate
racemase and its inhibitor (KRH) bt it gives an error like "Atom HD1 in
residue HIS 61 was not found in rtp entry HISB with 12 atomswhile sorting
atoms.For a hydrogen, this can be a different protonation state, or itmight
have had a different number in the PDB file and was rebuilt(it might for
instance have been H3, and we only expected H1 & H2).Note that hydrogens
might have been added to the entry for the N-terminus.Remove this hydrogen
or choose a different protonation state to solve it.Option -ignh will
ignore all hydrogens in the input."
where am i doing wrong.


Your H nomenclature doesn't match the expectations of the force field.  pdb2gmx 
has suggested a fix, which you should probably use.  Or ask Google, who knows 
all about different tips and tricks, since this gets asked and answered frequently.


-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] Md simulation error

[maria khan]

Hello dear gromacs users,
i m running md simulation for protein ligand complex that are glutamate
racemase and its inhibitor (KRH) bt it gives an error like "Atom HD1 in
residue HIS 61 was not found in rtp entry HISB with 12 atomswhile sorting
atoms.For a hydrogen, this can be a different protonation state, or itmight
have had a different number in the PDB file and was rebuilt(it might for
instance have been H3, and we only expected H1 & H2).Note that hydrogens
might have been added to the entry for the N-terminus.Remove this hydrogen
or choose a different protonation state to solve it.Option -ignh will
ignore all hydrogens in the input."
where am i doing wrong.
kindly help me out
Regards and thanks.
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