[gmx-users] Error in pdb2gmx

[Sadaf Rani]

Dear Gromacs users
I have tried to sort out this problem with gromacs 2020 and 2019 versions.
I gromacs 2019, It gives:-

All occupancies are one
Opening force field file ./amber99sb-ildn.ff/atomtypes.atp
Atomtype 106
Invalid format:
However, It generates a topology file.
In gromacs 2020, it gives:-

Program: gmx pdb2gmx, version 2020-UNCHECKED
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98)

Fatal error:
Invalid atomtype format: ''

I have modified my atomtypes.atp file as below:-

;[ atomtypes ]
; name  mass
nh 14.01
dnh 14.01
hn 1.008
dhn 1.008
ca 12.01
dca 12.01
nb 14.01
dnb 14.01
h5 1.008
dh5 1.008
nc 14.01
dnc 14.01
cd 12.01
dcd 12.01
na 14.01
dna 14.01
c3 12.01
dc3 12.01
h2 1.008
dh2 1.008
os 16
dos 16
h1 1.008
dh1 1.008
p5 30.97
dp5 30.97
o 16
do 16
oh 16
doh 16
ho 1.008
dho 1.008
h4 1.008
dh4 1.008
c 12.01
dc 12.01
n 14.01
dn 14.01
ha 1.008
dha 1.008
Atomtype 106 is ha, I cant find any thing wrong with it. Could you please
help me to fix this error?

Thanks.
Sadaf
-- 
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-requ...@gromacs.org.

Re: [gmx-users] Segmentation fault (core dumped) error during minimization

[Justin Lemkul]

On 4/19/20 4:38 PM, Elham Taghikhani wrote:

Thank you
I corrected the mdp file. As you said I opened my gro file in VMD but I didn't 
notice any bad contact around the atom.
Could you explain how can I observe bad contacts in the structure?


Calculate interatomic distances and look for anything very close to atom 
1996, check the topology to make sure sensible interactions will occur 
between that atom and its surroundings.



I even tried the different box size but it didn't work.


Box size is not relevant here.

-Justin


Both ligand and protein are ok with minimization separately.



On Apr 19, 2020, at 11:13 PM, Elham Taghikhani  wrote:


Hi
  
I am simulating a protein-ligand system, using oplss force field but i got this error during minimization.


Steepest Descents:
Tolerance (Fmax)   =  1.0e+03
Number of steps=5
Step=0, Dmax= 1.0e-02 nm, Epot=  1.27151e+33 Fmax= 4.76291e+07, atom= 1996
Segmentation fault (core dumped)

and this is my mpd file:
; LINES STARTING WITH ';' ARE COMMENTS
title   = Minimization  ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 
10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) 
steps to perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
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   = 1.2   ; Cut-off for making neighbor list 
(short range forces)
coulombtype = PME   ; Treatment of long range 
electrostatic interactions
rcoulomb= 1.2   ; long range electrostatic cut-off
vdwtype = cutoff
vdw-modifier= force-switch
rvdw-switch = 1.0
rvdw= 1.2   ; long range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions
DispCorr= no
Can anyone suggest how to troubleshoot this error?
The system is nuetralized.
  
Thank you in advance.




--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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-requ...@gromacs.org.

Re: [gmx-users] Segmentation fault (core dumped) error during minimization

[Elham Taghikhani]

Thank you
I corrected the mdp file. As you said I opened my gro file in VMD but I didn't 
notice any bad contact around the atom.
Could you explain how can I observe bad contacts in the structure?
I even tried the different box size but it didn't work.
Both ligand and protein are ok with minimization separately.


> On Apr 19, 2020, at 11:13 PM, Elham Taghikhani  wrote:
> 
> 
> Hi 
>  
> I am simulating a protein-ligand system, using oplss force field but i got 
> this error during minimization.
> 
> Steepest Descents:
>Tolerance (Fmax)   =  1.0e+03
>Number of steps=5
> Step=0, Dmax= 1.0e-02 nm, Epot=  1.27151e+33 Fmax= 4.76291e+07, atom= 1996
> Segmentation fault (core dumped)
> 
> and this is my mpd file:
> ; LINES STARTING WITH ';' ARE COMMENTS
> title = Minimization  ; Title of run
> 
> ; Parameters describing what to do, when to stop and what to save
> integrator= steep ; Algorithm (steep = steepest descent 
> minimization)
> emtol = 1000.0; Stop minimization when the maximum force < 
> 10.0 kJ/mol
> emstep  = 0.01  ; Energy step size
> nsteps= 5 ; Maximum number of 
> (minimization) steps to perform
> 
> ; Parameters describing how to find the neighbors of each atom and how to 
> calculate the interactions
> 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 = 1.2   ; Cut-off for making neighbor list 
> (short range forces)
> coulombtype   = PME   ; Treatment of long range 
> electrostatic interactions
> rcoulomb  = 1.2   ; long range electrostatic cut-off
> vdwtype = cutoff
> vdw-modifier= force-switch
> rvdw-switch = 1.0
> rvdw  = 1.2   ; long range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions
> DispCorr= no
> Can anyone suggest how to troubleshoot this error? 
> The system is nuetralized.
>  
> Thank you in advance.
> 
-- 
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-requ...@gromacs.org.

Re: [gmx-users] Artifact in pull-pbc-ref-prev-step-com

[Alex]

Any comment on this would be so appreciated!

Regards,
Alex

On Sat, Apr 18, 2020 at 2:12 PM Alex  wrote:

> Dear all,
> To generate the initial configurations for umbrella sampling, I conducted
> a simple pulling simulation by which a single-small molecule (mol_A) is
> being dragged along -Z from water into the body of a thin film.
> Since the thin film is large I used *"pull-pbc-ref-prev-step-com = yes"
> and "pull-group1-pbcatom  = -1"*  which cause a net shifting of the
> system along the pulling direction as soon as the mol_A reach to the thin
> film, please find below the pulling flags movie and  plot in below links.
>
> Centering the thin film and mol_A could solve the issue,  (echo 1 0 |
> trjconv -center yes) to some extent but still COM changes in the early
> stage below 2ns. ,
> COM:
> https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0
>
> Movie in which the water molecules are hidden:
> https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv
>
> -
> gmx version 2020.1
> -
> pull = yes
> pull-print-com   = no
> pull-print-ref-value = yes
> pull-print-components= Yes
> pull-nstxout = 1000
> pull-nstfout = 1000
> pull-pbc-ref-prev-step-com = yes
> pull-ngroups = 2
> pull-ncoords = 1
> pull-group1-name = Thin-film
> pull-group1-pbcatom  = -1
> pull-group2-name = mol_A
> pull-group2-pbcatom  = 0
> pull-coord1-type = umbrella
> pull-coord1-geometry = direction
> pull-coord1-groups   = 1 2
> pull-coord1-dim  = N N Y
> pull-coord1-origin   = 0.0 0.0 0.0
> pull-coord1-vec  = 0.0 0.0 -1.0
> pull-coord1-start= yes
> pull-coord1-init = 0
> pull-coord1-rate = 0.0005
> pull-coord1-k= 5000
> -
> I wonder if I could extract correct initial configuration from this
> trajectory? With correct initial configuration, I mean a set of gro file in
> which change from one from to another is the distance between the COM of
> the thin-film and mol_A?
>
> Thank you
> Alex
>
-- 
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-requ...@gromacs.org.

Re: [gmx-users] about correct methodology to run MD of small molecule in gromacs

[lazaro monteserin]

Thank you very much Dr. Lemkul for the advice

On Sun, Apr 19, 2020 at 5:33 PM Justin Lemkul  wrote:

>
>
> On 4/19/20 4:25 PM, lazaro monteserin wrote:
> > I thought this approach initially because I will refine the calculations
> > later at DFT level. What do you think?
>
> If you need a QM reference state for subsequent geometry refinement,
> just generate the QM-optimized geometry and start your calculations from
> that. You can then do an energy minimization with the force field to
> determine how well the molecular mechanics approximation agrees with QM
> (perhaps not very well as most nucleic acid force fields have not used
> DFT methods in their derivation).
>
> -Justin
>
> > On Sun, Apr 19, 2020 at 5:17 PM Justin Lemkul  wrote:
> >
> >>
> >> On 4/19/20 4:12 PM, lazaro monteserin wrote:
> >>> Dear Dr. Lemkul you are completely right. But then how could I approach
> >>> this problem to get an answer at the end that make sense?
> >> What is the purpose of requiring that the simulation start from the most
> >> stable vacuum conformation? There are very few rotatable bonds in a
> >> nucleoside and they are likely capable of fairly exhaustive sampling in
> >> water, anyway. The force field isn't designed for vacuum so anything you
> >> generate is likely to either be irrelevant in water or otherwise easily
> >> accessible in water in the first place.
> >>
> >> -Justin
> >>
> >>> On Sun, Apr 19, 2020 at 4:39 PM Justin Lemkul  wrote:
> >>>
>  On 4/18/20 7:39 PM, lazaro monteserin wrote:
> > Dear Gromacs users,
> >
> > As I have referred before I am simulating small molecules
> (nucleosides)
> > (around 33 atoms) in vacuum in Gromacs. When I do the simulations at
> >> the
> > end I want to select the most stable structure from the trajectory
> for
>  the
> > next steps.
> >
> > What would be the best methodology to use to run a molecular dynamics
> >> for
> > this?:
> >
> > 1) Run an anneling and collect the different frames for the
> trajectory
>  and
> > then at the end analyze the RSMD, free energy and maybe do clustering
> >> for
> > the different frames to select the most stable structure?
>  How do you propose to compute the conformational free energy? Note
> also
>  that no biomolecular force field is validated for use in the gas
> phase,
>  so the balance of conformational sampling has no guarantee of being
>  physically meaningful.
> 
> > 2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella
> > sampling"?, the only problem here is that I want all dihedral angles
> to
> > rotate and I do not know how to do this.
>  You can enforce dihedral rotation with the pull code, but the tutorial
>  has little use here aside from general concepts.
> 
> > 3) Do a procedure similar to tutorial 6 "Free energy of solvation" in
>  which
> > I generate the free energy from different lambda values from
> >> consecutive
> > simulations.
>  The tutorial is for decoupling a solute from water. You have a
> molecule
>  in vacuum. The only thing to decouple is the molecule itself, which
> will
>  give you an annihilated, physically nonsensical structure.
> 
>  -Justin
> 
>  --
>  ==
> 
>  Justin A. Lemkul, Ph.D.
>  Assistant Professor
>  Office: 301 Fralin Hall
>  Lab: 303 Engel Hall
> 
>  Virginia Tech Department of Biochemistry
>  340 West Campus Dr.
>  Blacksburg, VA 24061
> 
>  jalem...@vt.edu | (540) 231-3129
>  http://www.thelemkullab.com
> 
>  ==
> 
>  --
>  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-requ...@gromacs.org.
> 
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==
> >>
> >> --
> >> 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 

Re: [gmx-users] about correct methodology to run MD of small molecule in gromacs

[Justin Lemkul]

On 4/19/20 4:25 PM, lazaro monteserin wrote:

I thought this approach initially because I will refine the calculations
later at DFT level. What do you think?


If you need a QM reference state for subsequent geometry refinement, 
just generate the QM-optimized geometry and start your calculations from 
that. You can then do an energy minimization with the force field to 
determine how well the molecular mechanics approximation agrees with QM 
(perhaps not very well as most nucleic acid force fields have not used 
DFT methods in their derivation).


-Justin


On Sun, Apr 19, 2020 at 5:17 PM Justin Lemkul  wrote:



On 4/19/20 4:12 PM, lazaro monteserin wrote:

Dear Dr. Lemkul you are completely right. But then how could I approach
this problem to get an answer at the end that make sense?

What is the purpose of requiring that the simulation start from the most
stable vacuum conformation? There are very few rotatable bonds in a
nucleoside and they are likely capable of fairly exhaustive sampling in
water, anyway. The force field isn't designed for vacuum so anything you
generate is likely to either be irrelevant in water or otherwise easily
accessible in water in the first place.

-Justin


On Sun, Apr 19, 2020 at 4:39 PM Justin Lemkul  wrote:


On 4/18/20 7:39 PM, lazaro monteserin wrote:

Dear Gromacs users,

As I have referred before I am simulating small molecules (nucleosides)
(around 33 atoms) in vacuum in Gromacs. When I do the simulations at

the

end I want to select the most stable structure from the trajectory for

the

next steps.

What would be the best methodology to use to run a molecular dynamics

for

this?:

1) Run an anneling and collect the different frames for the trajectory

and

then at the end analyze the RSMD, free energy and maybe do clustering

for

the different frames to select the most stable structure?

How do you propose to compute the conformational free energy? Note also
that no biomolecular force field is validated for use in the gas phase,
so the balance of conformational sampling has no guarantee of being
physically meaningful.


2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella
sampling"?, the only problem here is that I want all dihedral angles to
rotate and I do not know how to do this.

You can enforce dihedral rotation with the pull code, but the tutorial
has little use here aside from general concepts.


3) Do a procedure similar to tutorial 6 "Free energy of solvation" in

which

I generate the free energy from different lambda values from

consecutive

simulations.

The tutorial is for decoupling a solute from water. You have a molecule
in vacuum. The only thing to decouple is the molecule itself, which will
give you an annihilated, physically nonsensical structure.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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-requ...@gromacs.org.


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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-requ...@gromacs.org.

Re: [gmx-users] about correct methodology to run MD of small molecule in gromacs

[lazaro monteserin]

I thought this approach initially because I will refine the calculations
later at DFT level. What do you think?

On Sun, Apr 19, 2020 at 5:17 PM Justin Lemkul  wrote:

>
>
> On 4/19/20 4:12 PM, lazaro monteserin wrote:
> > Dear Dr. Lemkul you are completely right. But then how could I approach
> > this problem to get an answer at the end that make sense?
>
> What is the purpose of requiring that the simulation start from the most
> stable vacuum conformation? There are very few rotatable bonds in a
> nucleoside and they are likely capable of fairly exhaustive sampling in
> water, anyway. The force field isn't designed for vacuum so anything you
> generate is likely to either be irrelevant in water or otherwise easily
> accessible in water in the first place.
>
> -Justin
>
> > On Sun, Apr 19, 2020 at 4:39 PM Justin Lemkul  wrote:
> >
> >>
> >> On 4/18/20 7:39 PM, lazaro monteserin wrote:
> >>> Dear Gromacs users,
> >>>
> >>> As I have referred before I am simulating small molecules (nucleosides)
> >>> (around 33 atoms) in vacuum in Gromacs. When I do the simulations at
> the
> >>> end I want to select the most stable structure from the trajectory for
> >> the
> >>> next steps.
> >>>
> >>> What would be the best methodology to use to run a molecular dynamics
> for
> >>> this?:
> >>>
> >>> 1) Run an anneling and collect the different frames for the trajectory
> >> and
> >>> then at the end analyze the RSMD, free energy and maybe do clustering
> for
> >>> the different frames to select the most stable structure?
> >> How do you propose to compute the conformational free energy? Note also
> >> that no biomolecular force field is validated for use in the gas phase,
> >> so the balance of conformational sampling has no guarantee of being
> >> physically meaningful.
> >>
> >>> 2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella
> >>> sampling"?, the only problem here is that I want all dihedral angles to
> >>> rotate and I do not know how to do this.
> >> You can enforce dihedral rotation with the pull code, but the tutorial
> >> has little use here aside from general concepts.
> >>
> >>> 3) Do a procedure similar to tutorial 6 "Free energy of solvation" in
> >> which
> >>> I generate the free energy from different lambda values from
> consecutive
> >>> simulations.
> >> The tutorial is for decoupling a solute from water. You have a molecule
> >> in vacuum. The only thing to decouple is the molecule itself, which will
> >> give you an annihilated, physically nonsensical structure.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==
> >>
> >> --
> >> 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-requ...@gromacs.org.
> >>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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-requ...@gromacs.org.
>
-- 
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-requ...@gromacs.org.

Re: [gmx-users] about correct methodology to run MD of small molecule in gromacs

[Justin Lemkul]

On 4/19/20 4:12 PM, lazaro monteserin wrote:

Dear Dr. Lemkul you are completely right. But then how could I approach
this problem to get an answer at the end that make sense?


What is the purpose of requiring that the simulation start from the most 
stable vacuum conformation? There are very few rotatable bonds in a 
nucleoside and they are likely capable of fairly exhaustive sampling in 
water, anyway. The force field isn't designed for vacuum so anything you 
generate is likely to either be irrelevant in water or otherwise easily 
accessible in water in the first place.


-Justin


On Sun, Apr 19, 2020 at 4:39 PM Justin Lemkul  wrote:



On 4/18/20 7:39 PM, lazaro monteserin wrote:

Dear Gromacs users,

As I have referred before I am simulating small molecules (nucleosides)
(around 33 atoms) in vacuum in Gromacs. When I do the simulations at the
end I want to select the most stable structure from the trajectory for

the

next steps.

What would be the best methodology to use to run a molecular dynamics for
this?:

1) Run an anneling and collect the different frames for the trajectory

and

then at the end analyze the RSMD, free energy and maybe do clustering for
the different frames to select the most stable structure?

How do you propose to compute the conformational free energy? Note also
that no biomolecular force field is validated for use in the gas phase,
so the balance of conformational sampling has no guarantee of being
physically meaningful.


2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella
sampling"?, the only problem here is that I want all dihedral angles to
rotate and I do not know how to do this.

You can enforce dihedral rotation with the pull code, but the tutorial
has little use here aside from general concepts.


3) Do a procedure similar to tutorial 6 "Free energy of solvation" in

which

I generate the free energy from different lambda values from consecutive
simulations.

The tutorial is for decoupling a solute from water. You have a molecule
in vacuum. The only thing to decouple is the molecule itself, which will
give you an annihilated, physically nonsensical structure.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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-requ...@gromacs.org.

Re: [gmx-users] about correct methodology to run MD of small molecule in gromacs

[lazaro monteserin]

Dear Dr. Lemkul you are completely right. But then how could I approach
this problem to get an answer at the end that make sense?

On Sun, Apr 19, 2020 at 4:39 PM Justin Lemkul  wrote:

>
>
> On 4/18/20 7:39 PM, lazaro monteserin wrote:
> > Dear Gromacs users,
> >
> > As I have referred before I am simulating small molecules (nucleosides)
> > (around 33 atoms) in vacuum in Gromacs. When I do the simulations at the
> > end I want to select the most stable structure from the trajectory for
> the
> > next steps.
> >
> > What would be the best methodology to use to run a molecular dynamics for
> > this?:
> >
> > 1) Run an anneling and collect the different frames for the trajectory
> and
> > then at the end analyze the RSMD, free energy and maybe do clustering for
> > the different frames to select the most stable structure?
>
> How do you propose to compute the conformational free energy? Note also
> that no biomolecular force field is validated for use in the gas phase,
> so the balance of conformational sampling has no guarantee of being
> physically meaningful.
>
> > 2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella
> > sampling"?, the only problem here is that I want all dihedral angles to
> > rotate and I do not know how to do this.
>
> You can enforce dihedral rotation with the pull code, but the tutorial
> has little use here aside from general concepts.
>
> > 3) Do a procedure similar to tutorial 6 "Free energy of solvation" in
> which
> > I generate the free energy from different lambda values from consecutive
> > simulations.
>
> The tutorial is for decoupling a solute from water. You have a molecule
> in vacuum. The only thing to decouple is the molecule itself, which will
> give you an annihilated, physically nonsensical structure.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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-requ...@gromacs.org.
>
-- 
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-requ...@gromacs.org.

Re: [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6

[Paolo Costa]

It was a typos. In the .pdb file I wrote SnC as residue name, while in .rtp
file it was still written SnCl. That's why the error.
Thanks a lot again.

Paolo

Il dom 19 apr 2020, 22:05 Justin Lemkul  ha scritto:

>
>
> On 4/19/20 3:47 PM, Paolo Costa wrote:
> > Hi Justin,
> >
> > I could fix the issue.
> >
> > Thanks again for your help.
>
> And in the spirit of helping others that use this mailing list, what
> exactly was the problem and how did you solve it?
>
> -Justin
>
> > Paolo
> >
> > Il giorno dom 19 apr 2020 alle ore 21:35 Justin Lemkul 
> ha
> > scritto:
> >
> >>
> >> On 4/17/20 5:25 PM, Paolo Costa wrote:
> >>> Hi Justin,
> >>>
> >>> thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my
> >>> stannate.pdb and also to stannate.rtp. But still I get the error.
> >>> Here the output file of from pdb2gmx:
> >>>
> >>> Opening force field file
> /usr/share/gromacs/top/amber99.ff/aminoacids.r2b
> >>> Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b
> >>> Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b
> >>> Reading stannate.pdb...
> >>> WARNING: all CONECT records are ignored
> >>> Read 'stannate', 7 atoms
> >>> Analyzing pdb file
> >>> Splitting chemical chains based on TER records or chain id changing.
> >>> There are 1 chains and 0 blocks of water and 1 residues with 7 atoms
> >>>
> >>> chain  #res #atoms
> >>> 1 ' ' 1  7
> >>>
> >>> All occupancy fields zero. This is probably not an X-Ray structure
> >>> Opening force field file
> /usr/share/gromacs/top/amber99.ff/atomtypes.atp
> >>> Atomtype 68
> >>> Reading residue database... (amber99)
> >>> Opening force field file
> /usr/share/gromacs/top/amber99.ff/aminoacids.rtp
> >>> Residue 93
> >>> Sorting it all out...
> >>> Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp
> >>> Residue 94
> >>> Sorting it all out...
> >>> Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp
> >>> Residue 110
> >>> Sorting it all out...
> >>> Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp
> >>> Residue 126
> >>> Sorting it all out...
> >>> Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp
> >>> Residue 127
> >>> Sorting it all out...
> >>> Opening force field file
> /usr/share/gromacs/top/amber99.ff/aminoacids.hdb
> >>> Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb
> >>> Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb
> >>> Opening force field file
> >> /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb
> >>> Opening force field file
> >> /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb
> >>> Back Off! I just backed up topol.top to ./#topol.top.19#
> >>> Processing chain 1 (7 atoms, 1 residues)
> >>>
> >>> Warning: Starting residue SnC0 in chain not identified as
> >> Protein/RNA/DNA.
> >>> This chain lacks identifiers, which makes it impossible to do strict
> >>> classification of the start/end residues. Here we need to guess this
> >> residue
> >>> should not be part of the chain and instead introduce a break, but that
> >> will
> >>> be catastrophic if they should in fact be linked. Please check your
> >>> structure,
> >>> and add SnC to residuetypes.dat if this was not correct.
> >>>
> >>> Problem with chain definition, or missing terminal residues.
> >>> This chain does not appear to contain a recognized chain molecule.
> >>> If this is incorrect, you can edit residuetypes.dat to modify the
> >> behavior.
> >>> 8 out of 8 lines of specbond.dat converted successfully
> >>>
> >>> ---
> >>> Program: gmx pdb2gmx, version 2018.1
> >>> Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639)
> >>>
> >>> Fatal error:
> >>> Residue 'SnC' not found in residue topology database
> >>>
> >>> *Thanks a lot for helping!*
> >> Without seeing the contents of the PDB file and stannate.rtp, there's
> >> not much to go on here.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==
> >>
> >> --
> >> 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-requ...@gromacs.org.
> >>
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> 

Re: [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6

[Justin Lemkul]

On 4/19/20 3:47 PM, Paolo Costa wrote:

Hi Justin,

I could fix the issue.

Thanks again for your help.


And in the spirit of helping others that use this mailing list, what 
exactly was the problem and how did you solve it?


-Justin


Paolo

Il giorno dom 19 apr 2020 alle ore 21:35 Justin Lemkul  ha
scritto:



On 4/17/20 5:25 PM, Paolo Costa wrote:

Hi Justin,

thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my
stannate.pdb and also to stannate.rtp. But still I get the error.
Here the output file of from pdb2gmx:

Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b
Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b
Reading stannate.pdb...
WARNING: all CONECT records are ignored
Read 'stannate', 7 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 1 residues with 7 atoms

chain  #res #atoms
1 ' ' 1  7

All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file /usr/share/gromacs/top/amber99.ff/atomtypes.atp
Atomtype 68
Reading residue database... (amber99)
Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp
Residue 94
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp
Residue 110
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp
Residue 126
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp
Residue 127
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb
Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb
Opening force field file

/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb

Opening force field file

/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.19#
Processing chain 1 (7 atoms, 1 residues)

Warning: Starting residue SnC0 in chain not identified as

Protein/RNA/DNA.

This chain lacks identifiers, which makes it impossible to do strict
classification of the start/end residues. Here we need to guess this

residue

should not be part of the chain and instead introduce a break, but that

will

be catastrophic if they should in fact be linked. Please check your
structure,
and add SnC to residuetypes.dat if this was not correct.

Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the

behavior.

8 out of 8 lines of specbond.dat converted successfully

---
Program: gmx pdb2gmx, version 2018.1
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639)

Fatal error:
Residue 'SnC' not found in residue topology database

*Thanks a lot for helping!*

Without seeing the contents of the PDB file and stannate.rtp, there's
not much to go on here.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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-requ...@gromacs.org.





--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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-requ...@gromacs.org.

Re: [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6

[Paolo Costa]

Hi Justin,

I could fix the issue.

Thanks again for your help.

Paolo

Il giorno dom 19 apr 2020 alle ore 21:35 Justin Lemkul  ha
scritto:

>
>
> On 4/17/20 5:25 PM, Paolo Costa wrote:
> > Hi Justin,
> >
> > thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my
> > stannate.pdb and also to stannate.rtp. But still I get the error.
> > Here the output file of from pdb2gmx:
> >
> > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.r2b
> > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b
> > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b
> > Reading stannate.pdb...
> > WARNING: all CONECT records are ignored
> > Read 'stannate', 7 atoms
> > Analyzing pdb file
> > Splitting chemical chains based on TER records or chain id changing.
> > There are 1 chains and 0 blocks of water and 1 residues with 7 atoms
> >
> >chain  #res #atoms
> >1 ' ' 1  7
> >
> > All occupancy fields zero. This is probably not an X-Ray structure
> > Opening force field file /usr/share/gromacs/top/amber99.ff/atomtypes.atp
> > Atomtype 68
> > Reading residue database... (amber99)
> > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.rtp
> > Residue 93
> > Sorting it all out...
> > Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp
> > Residue 94
> > Sorting it all out...
> > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp
> > Residue 110
> > Sorting it all out...
> > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp
> > Residue 126
> > Sorting it all out...
> > Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp
> > Residue 127
> > Sorting it all out...
> > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.hdb
> > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb
> > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb
> > Opening force field file
> /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb
> > Opening force field file
> /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb
> >
> > Back Off! I just backed up topol.top to ./#topol.top.19#
> > Processing chain 1 (7 atoms, 1 residues)
> >
> > Warning: Starting residue SnC0 in chain not identified as
> Protein/RNA/DNA.
> > This chain lacks identifiers, which makes it impossible to do strict
> > classification of the start/end residues. Here we need to guess this
> residue
> > should not be part of the chain and instead introduce a break, but that
> will
> > be catastrophic if they should in fact be linked. Please check your
> > structure,
> > and add SnC to residuetypes.dat if this was not correct.
> >
> > Problem with chain definition, or missing terminal residues.
> > This chain does not appear to contain a recognized chain molecule.
> > If this is incorrect, you can edit residuetypes.dat to modify the
> behavior.
> > 8 out of 8 lines of specbond.dat converted successfully
> >
> > ---
> > Program: gmx pdb2gmx, version 2018.1
> > Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639)
> >
> > Fatal error:
> > Residue 'SnC' not found in residue topology database
> >
> > *Thanks a lot for helping!*
>
> Without seeing the contents of the PDB file and stannate.rtp, there's
> not much to go on here.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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-requ...@gromacs.org.
>


-- 
Paolo Costa, Ph.D.
Postdoctoral Researcher
Department of Chemistry and Biomolecular Sciences
University of Ottawa
10 Marie Curie, Ottawa, ON K1N 6N5, Canada
Room number: DRO 326 (D'Iorio Hall)
-- 
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-requ...@gromacs.org.

Re: [gmx-users] Installation on iPad

[Ali Khodayari]

Dear Marko,

Thank you for your response. Indeed SSH would be already proper help. I am
also interested to see whether I can run GROMACS on itself as well. 
I came through a shell for iPad, called Blink Shell, which seems to be able
to cover some aspects of coding, but I am not sure if it would be able to
host gmx too. It is paid btw.

My best,
Ali



-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 On Behalf Of Marko
Petrovic
Sent: zondag 19 april 2020 19:09
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Installation on iPad

You can at least run SSH clients on iOS so you can technically edit text
files and run commands from it even if the execution is not on the iPad.

With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science KTH Royal Institute of
Technology

On 18 Apr 2020, at 14:43, Ali Khodayari
mailto:ali.khoday...@student.kuleuven.be>
> wrote:

Dear gmx users,



I would like to ask whether it is possible to install GROMACS on iPad as
well? Obviously I am not trying to run any simulations on it, but to be able
to generate the run files and to transfer them to a cluster. Does it work
the same way you'll have it on any other MacOS? Of course, considering the
new iPad OS released.



Kind regards,

Ali



--
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-requ...@gromacs.org.

--
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-requ...@gromacs.org.

-- 
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-requ...@gromacs.org.

Re: [gmx-users] Failed to find GROMACS magic number in trr frame header

[Justin Lemkul]

On 4/18/20 5:38 AM, Mijiddorj B wrote:

Dear Justin,

Thank you very much for your reply. I see. However, I have one more
question. Is it caused by usage of -noappend or other reasons?


No, it's because of the power failure likely causing an issue on the 
filesystem or with your file directly.


-Justin


Best regards,

Mijiddorj

-

Message: 1
Date: Fri, 17 Apr 2020 11:51:25 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Failed to find GROMACS magic number in trr
 frame header
Message-ID: <77b40330-739a-c03e-85f2-1bc74b97c...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 4/17/20 10:13 AM, Mijiddorj B wrote:

Dear GMX users,

Hello, I performed MD simulation using gromacs 2018.7v. During this
simulation, the calculation was stopped because of the electric cut.

Then,

I continued the simulation using "gmx mdrun with -noappend" in order to

get

separate trajectory for the safety of data. After that, I would like to
concatenate the trr files.
However, I received following error message.

How, can I concatenate these trajectories.
**
Program: gmx trjcat, version 2018.7
Source file: src/gromacs/fileio/trrio.cpp (line 114)

Fatal error:
Failed to find GROMACS magic number in trr frame header, so this is not a
trr
file!

For more information and tips for troubleshooting, please check the

GROMACS

website at http://www.gromacs.org/Documentation/Errors


Your file is corrupted and you will have to run that portion of the
simulation again.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==




--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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-requ...@gromacs.org.

Re: [gmx-users] Segmentation fault (core dumped) error during minimization

[Justin Lemkul]

On 4/19/20 2:43 PM, Elham Taghikhani wrote:

Hi
  I am simulating a protein-ligand system, using oplss force field but i got 
this error during minimization.
Steepest Descents:
    Tolerance (Fmax)   =  1.0e+03
    Number of steps    =    5
Step=    0, Dmax= 1.0e-02 nm, Epot=  1.27151e+33 Fmax= 4.76291e+07, atom= 1996


Look for bad contacts around atom 1996.


Segmentation fault (core dumped)

and this is my mpd file:; LINES STARTING WITH ';' ARE COMMENTS
title   = Minimization  ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 
10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) 
steps to perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
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   = 1.2   ; Cut-off for making neighbor list 
(short range forces)
coulombtype = PME   ; Treatment of long range 
electrostatic interactions
rcoulomb= 1.2   ; long range electrostatic cut-off
vdwtype = cutoff
vdw-modifier= force-switch
rvdw-switch = 1.0
rvdw= 1.2   ; long range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions
DispCorr= no
Can anyone suggest how to troubleshoot this error?


Your cutoffs are for the CHARMM force field, not OPLS. This isn't the 
source of the error, but you are using the force field incorrectly.


Other than that, protein-ligand complexes are specifically addressed in 
the troubleshooting section of 
http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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-requ...@gromacs.org.

Re: [gmx-users] about correct methodology to run MD of small molecule in gromacs

[Justin Lemkul]

On 4/18/20 7:39 PM, lazaro monteserin wrote:

Dear Gromacs users,

As I have referred before I am simulating small molecules (nucleosides)
(around 33 atoms) in vacuum in Gromacs. When I do the simulations at the
end I want to select the most stable structure from the trajectory for the
next steps.

What would be the best methodology to use to run a molecular dynamics for
this?:

1) Run an anneling and collect the different frames for the trajectory and
then at the end analyze the RSMD, free energy and maybe do clustering for
the different frames to select the most stable structure?


How do you propose to compute the conformational free energy? Note also 
that no biomolecular force field is validated for use in the gas phase, 
so the balance of conformational sampling has no guarantee of being 
physically meaningful.



2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella
sampling"?, the only problem here is that I want all dihedral angles to
rotate and I do not know how to do this.


You can enforce dihedral rotation with the pull code, but the tutorial 
has little use here aside from general concepts.



3) Do a procedure similar to tutorial 6 "Free energy of solvation" in which
I generate the free energy from different lambda values from consecutive
simulations.


The tutorial is for decoupling a solute from water. You have a molecule 
in vacuum. The only thing to decouple is the molecule itself, which will 
give you an annihilated, physically nonsensical structure.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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-requ...@gromacs.org.

Re: [gmx-users] Regarding use of harmonic wall model

[Justin Lemkul]

On 4/18/20 4:43 AM, Shashank Ranjan Srivastava wrote:

Hello everyone,
I want to create a gap  between the first and last strand of a beta barrel
so that I can put a new strand in between.
So, I have generated an input file using charmm-gui and using its gromacs
production file (production.mdp) to run the simulation. I want to use a
harmonic wall model to disrupt the bonding between the first and last
strand of the beta barrel but not getting how to do it .
I have asked it before as well but I did not get any suggestion.
Please kindly help me with this query if anybody has any idea regarding
this.


I suggest using the pull code. The implementation of walls in GROMACS 
does not do what you're asking.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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-requ...@gromacs.org.

Re: [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6

[Justin Lemkul]

On 4/17/20 5:25 PM, Paolo Costa wrote:

Hi Justin,

thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my
stannate.pdb and also to stannate.rtp. But still I get the error.
Here the output file of from pdb2gmx:

Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b
Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b
Reading stannate.pdb...
WARNING: all CONECT records are ignored
Read 'stannate', 7 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 1 residues with 7 atoms

   chain  #res #atoms
   1 ' ' 1  7

All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file /usr/share/gromacs/top/amber99.ff/atomtypes.atp
Atomtype 68
Reading residue database... (amber99)
Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp
Residue 94
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp
Residue 110
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp
Residue 126
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp
Residue 127
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb
Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb
Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.19#
Processing chain 1 (7 atoms, 1 residues)

Warning: Starting residue SnC0 in chain not identified as Protein/RNA/DNA.
This chain lacks identifiers, which makes it impossible to do strict
classification of the start/end residues. Here we need to guess this residue
should not be part of the chain and instead introduce a break, but that will
be catastrophic if they should in fact be linked. Please check your
structure,
and add SnC to residuetypes.dat if this was not correct.

Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

---
Program: gmx pdb2gmx, version 2018.1
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639)

Fatal error:
Residue 'SnC' not found in residue topology database

*Thanks a lot for helping!*


Without seeing the contents of the PDB file and stannate.rtp, there's 
not much to go on here.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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-requ...@gromacs.org.

[gmx-users] Segmentation fault (core dumped) error during minimization

[Elham Taghikhani]

Hi 
 I am simulating a protein-ligand system, using oplss force field but i got 
this error during minimization.
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps    =    5
Step=    0, Dmax= 1.0e-02 nm, Epot=  1.27151e+33 Fmax= 4.76291e+07, atom= 1996
Segmentation fault (core dumped)

and this is my mpd file:; LINES STARTING WITH ';' ARE COMMENTS
title   = Minimization  ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 
10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) 
steps to perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
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   = 1.2   ; Cut-off for making neighbor list 
(short range forces)
coulombtype = PME   ; Treatment of long range 
electrostatic interactions
rcoulomb= 1.2   ; long range electrostatic cut-off
vdwtype = cutoff
vdw-modifier= force-switch
rvdw-switch = 1.0
rvdw= 1.2   ; long range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions
DispCorr= no
Can anyone suggest how to troubleshoot this error? 
The system is nuetralized. Thank you in advance.

-- 
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-requ...@gromacs.org.

Re: [gmx-users] atomselection for index group of cyclic rings

[Archana Sonawani-Jagtap]

Hi,

First make index file of the atoms involved in rings and then use following
command:
gmx distance -f .xtc -s .tpr -n .ndx -select 'cog of group " group 1" plus
cog of group "group2"' -oav .xvg

Hope this helps

Thanks
Archana


On Fri, Apr 17, 2020 at 10:25 AM Prasanth G, Research Scholar <
prasanthgha...@sssihl.edu.in> wrote:

> Dear all,
> I am interested in measuring the distance between two cyclic rings present
> in the residues and ligands over time. Can you kindly suggest how to go
> about this?
> Specially, if i am interested in measuring the distance between the center
> of the two rings over time. Thank you
>
> --
> Regards,
> Prasanth.
> --
> 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-requ...@gromacs.org.
>
-- 
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-requ...@gromacs.org.

Re: [gmx-users] Installation on iPad

[Marko Petrovic]

You can at least run SSH clients on iOS so you can technically edit text files 
and run commands from it even if the execution is not on the iPad.

With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology

On 18 Apr 2020, at 14:43, Ali Khodayari 
mailto:ali.khoday...@student.kuleuven.be>> 
wrote:

Dear gmx users,



I would like to ask whether it is possible to install GROMACS on iPad as
well? Obviously I am not trying to run any simulations on it, but to be able
to generate the run files and to transfer them to a cluster. Does it work
the same way you'll have it on any other MacOS? Of course, considering the
new iPad OS released.



Kind regards,

Ali



--
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-requ...@gromacs.org.

-- 
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-requ...@gromacs.org.

Re: [gmx-users] error in pdb2gmx

[Sadaf Rani]

Dear Gromacs users
I have tried to sort out this problem with gromacs 2020 and 2019 versions.
I gromacs 2019, It gives:-

All occupancies are one
Opening force field file ./amber99sb-ildn.ff/atomtypes.atp
Atomtype 106
Invalid format:
However, It generates a topology file.
In gromacs 2020, it gives:-

Program: gmx pdb2gmx, version 2020-UNCHECKED
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98)

Fatal error:
Invalid atomtype format: ''

I have modified my atomtypes.atp file as below:-

;[ atomtypes ]
; name  mass
nh 14.01
dnh 14.01
hn 1.008
dhn 1.008
ca 12.01
dca 12.01
nb 14.01
dnb 14.01
h5 1.008
dh5 1.008
nc 14.01
dnc 14.01
cd 12.01
dcd 12.01
na 14.01
dna 14.01
c3 12.01
dc3 12.01
h2 1.008
dh2 1.008
os 16
dos 16
h1 1.008
dh1 1.008
p5 30.97
dp5 30.97
o 16
do 16
oh 16
doh 16
ho 1.008
dho 1.008
h4 1.008
dh4 1.008
c 12.01
dc 12.01
n 14.01
dn 14.01
ha 1.008
dha 1.008
Atomtype 106 is ha, I cant find any thing wrong with it. Could you please
help me to fix this error?

Thanks.
Sadaf
-- 
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-requ...@gromacs.org.

Re: [gmx-users] Question about Mean Square Displacement (MSD)

[Kevin Boyd]

Can you send links to the results Gromacs gives you and the results you're
getting, along with the code that you're using to calculate the MSD?

On Sun, Apr 19, 2020 at 2:38 AM Sina Omrani  wrote:

> *Message sent from a system outside of UConn.*
>
>
> Dear Kevin, Thanks for your suggestions but the problem is the difference
> between my answer and GROMACS in calculated MSD. I performed 6 ns
> simulation just for checking my MSD results and I'm not going to calculate
> the diffusion coefficient from it.
>
> On Sun, 19 Apr 2020 at 02:33, Kevin Boyd  wrote:
>
> > What are you trying to calculate MSD for? I doubt that would be
> sufficient
> > sampling to calculate the diffusion coefficient of anything except maybe
> > water. For lipids, you don't start getting accurate readings until you
> > reach a **lag** time of 10 ns, and you need 100s of ns of data to get a
> > good reading even at that lag time. That's with many lipids in a
> bilayer. I
> > don't have experience with calculating diffusion coefficients for
> > proteins, but I'd imagine you need microseconds of sampling, since
> they're
> > much slower tumblers and you usually only have one per simulation box.
> >
> > Your save rate is fine, and could be even more granular.
> >
> > On Sat, Apr 18, 2020 at 12:54 PM Sina Omrani 
> > wrote:
> >
> > > *Message sent from a system outside of UConn.*
> > >
> > >
> > > Thanks, Kevin,
> > > I am looking for the MSD vs lag plot. I use the saved frames that
> > specified
> > > in mdp file. Is that the problem? I saved positions every 10 ps for a
> > 6000
> > > ps simulation. should I lower this or is there another way for using
> more
> > > trajectories?
> > >
> > > On Sun, 19 Apr 2020 at 00:10, Kevin Boyd  wrote:
> > >
> > > > Hi,
> > > >
> > > > Are you talking about the reported diffusion coefficient or the MSD
> vs
> > > lag
> > > > plot? You should be very careful about where you fit. By default,
> > Gromacs
> > > > calculates MSDs at much longer lag times than you typically have good
> > > data
> > > > for. Use the -beginfit and -endfit options to restrict the fit to the
> > lag
> > > > times where the MSD plot is linear.
> > > >
> > > > >I use trjconv command and use the output .gro file
> > > >
> > > > This doesn't make much sense, how many frames are you analyzing?
> > > >
> > > >
> > > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth  >
> > > > wrote:
> > > >
> > > > > *Message sent from a system outside of UConn.*
> > > > >
> > > > >
> > > > > Unless you give you give details how you calculate the MSD it will
> > not
> > > be
> > > > > possible to help.
> > > > > Are you using unwrapped co-ordinates in your calculations for MSD?
> > > > >
> > > > > Arun
> > > > >
> > > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani <
> sinaomran...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > > I am trying to post-processing my results and calculate MSD (mean
> > > > square
> > > > > > displacement) but my answer is different from the MSD value that
> > > > GROMACS
> > > > > > calculated. I use trjconv command and use the output .gro file. I
> > > tried
> > > > > to
> > > > > > understand the GROMACS code but I am not a good programmer. Is
> > there
> > > > any
> > > > > > specific detail except the Einstein relation in the manual?
> > > > > >
> > > > > > sorry if here is not the right place to ask this question.
> > > > > > Best regards.
> > > > > >
> > > > > > Sina Omrani.
> > > > > > --
> > > > > > 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-requ...@gromacs.org.
> > > > > >
> > > > > --
> > > > > 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-requ...@gromacs.org.
> > > > >
> > > > --
> > > > 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-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > 

[gmx-users] error in pdb2gmx

[Sadaf Rani]

Dear Gromacs users
I am facing a strange problem while doing pdb2gmx:-
When I use the command:-
 gmx pdb2gmx -f 74A-G.pdb -o 74A-G.gro
It shows the following:-
going to rename ./amber99sb-ildn.ff/aminoacids.r2b
Opening force field file ./amber99sb-ildn.ff/aminoacids.r2b
going to rename ./amber99sb-ildn.ff/dna.r2b
Opening force field file ./amber99sb-ildn.ff/dna.r2b
going to rename ./amber99sb-ildn.ff/rna.r2b
Opening force field file ./amber99sb-ildn.ff/rna.r2b
Reading 74A-G.pdb...
Read '', 4082 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 2 chains and 0 blocks of water and 492 residues with 4082 atoms

  chain  #res #atoms
  1 'A'   489   3970
  2 'B' 3112

All occupancies are one
Opening force field file ./amber99sb-ildn.ff/atomtypes.atp

---
Program: gmx pdb2gmx, version 2020-UNCHECKED
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98)

Fatal error:
Invalid atomtype format: ''

However, when I use without gmx, as below:-
pdb2gmx -f 74A-G.pdb -o 74A-G.gro
It generates topology file successfully. What's wrong with the format in
atomtypes.atp I am unable to understand. Could you please help me to find
out?
I have added a new residue to my forcefield file as mentioned in gromacs
manual.
Please correct me where I am wrong, I have added following in
atomtypes.atp file:-
;[ atomtypes ]
; name   bond_type   mass  chargeptype  sigma  eps
  nh 14.01000 0.000   A 3.25000e-1   7.11280e-1
  hn  1.00800 0.000   A 1.06908e-1   6.56888e-2
  ca 12.01000 0.000   A 3.39967e-1   3.59824e-1
  nb 14.01000 0.000   A 3.25000e-1   7.11280e-1
  h5  1.00800 0.000   A 2.42146e-1   6.27600e-2
  nc 14.01000 0.000   A 3.25000e-1   7.11280e-1
  cd 12.01000 0.000   A 3.39967e-1   3.59824e-1
  na 14.01000 0.000   A 3.25000e-1   7.11280e-1
  c3 12.01000 0.000   A 3.39967e-1   4.57730e-1
  h2  1.00800 0.000   A 2.29317e-1   6.56888e-2
  os 16.0 0.000   A 3.1e-1   7.11280e-1
  h1  1.00800 0.000   A 2.47135e-1   6.56888e-2
  p5 30.97000 0.000   A 3.74177e-1   8.36800e-1
   o 16.0 0.000   A 2.95992e-1   8.78640e-1
  oh 16.0 0.000   A 3.06647e-1   8.80314e-1
  ho  1.00800 0.000   A 0.0e+0   0.0e+0
  h4  1.00800 0.000   A 2.51055e-1   6.27600e-2
   c 12.01000 0.000   A 3.39967e-1   3.59824e-1
   n 14.01000 0.000   A 3.25000e-1   7.11280e-1
  ha  1.00800 0.000   A 2.59964e-1   6.27600e-2

Thanks.

Sadaf
-- 
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-requ...@gromacs.org.

Re: [gmx-users] atomtype "OE" in charmm36

[Schirra, Simone]

I figured it out myself. It seems like it's calles "OC30A" now. My energy 
minimization problems came from somewhere else and I have now been able to 
solve them.
Excuse me for asking this, kind of obvious, question.

Simone

Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] im Auftrag von 
Justin Lemkul [jalem...@vt.edu]
Gesendet: Freitag, 17. April 2020 13:10
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] atomtype "OE" in charmm36

On 4/17/20 4:45 AM, Schirra, Simone wrote:
> Dear Gromacs users,
>
> I want to simulate polyethylene glycol and I am using a script to build my 
> .itp and .gro files. The script is designed to work with charmm35r, however I 
> only found charmm36 available now (I read, that c35r was only temporary). I 
> thought, it should work with this version as well.
> When I try energy minimization, the atomtype OE is not found. OE is used for 
> the ether oxygen's in the itp file.
> I also found an ether toppar file at MacKerell Lab Hompage, however it seems 
> to be designed for use with charmm rather than gromacs.

Which toppar file are you trying to use?

> Is there a way to convert it for use with gromacs? Or is there another 
> definition I can use to work with my PEG? Or maybe c35r is still somewhere 
> around?

C35r became C36 in official implementation. Likely the atom type just
got renamed or assumed into an existing one, but without knowing which
topology you're using, I can't comment. The PEO "toppar_ether" from
Alex's site doesn't have anything called OE in it.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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-requ...@gromacs.org.
-- 
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-requ...@gromacs.org.

Re: [gmx-users] Question about Mean Square Displacement (MSD)

[Sina Omrani]

Dear Kevin, Thanks for your suggestions but the problem is the difference
between my answer and GROMACS in calculated MSD. I performed 6 ns
simulation just for checking my MSD results and I'm not going to calculate
the diffusion coefficient from it.

On Sun, 19 Apr 2020 at 02:33, Kevin Boyd  wrote:

> What are you trying to calculate MSD for? I doubt that would be sufficient
> sampling to calculate the diffusion coefficient of anything except maybe
> water. For lipids, you don't start getting accurate readings until you
> reach a **lag** time of 10 ns, and you need 100s of ns of data to get a
> good reading even at that lag time. That's with many lipids in a bilayer. I
> don't have experience with calculating diffusion coefficients for
> proteins, but I'd imagine you need microseconds of sampling, since they're
> much slower tumblers and you usually only have one per simulation box.
>
> Your save rate is fine, and could be even more granular.
>
> On Sat, Apr 18, 2020 at 12:54 PM Sina Omrani 
> wrote:
>
> > *Message sent from a system outside of UConn.*
> >
> >
> > Thanks, Kevin,
> > I am looking for the MSD vs lag plot. I use the saved frames that
> specified
> > in mdp file. Is that the problem? I saved positions every 10 ps for a
> 6000
> > ps simulation. should I lower this or is there another way for using more
> > trajectories?
> >
> > On Sun, 19 Apr 2020 at 00:10, Kevin Boyd  wrote:
> >
> > > Hi,
> > >
> > > Are you talking about the reported diffusion coefficient or the MSD vs
> > lag
> > > plot? You should be very careful about where you fit. By default,
> Gromacs
> > > calculates MSDs at much longer lag times than you typically have good
> > data
> > > for. Use the -beginfit and -endfit options to restrict the fit to the
> lag
> > > times where the MSD plot is linear.
> > >
> > > >I use trjconv command and use the output .gro file
> > >
> > > This doesn't make much sense, how many frames are you analyzing?
> > >
> > >
> > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth 
> > > wrote:
> > >
> > > > *Message sent from a system outside of UConn.*
> > > >
> > > >
> > > > Unless you give you give details how you calculate the MSD it will
> not
> > be
> > > > possible to help.
> > > > Are you using unwrapped co-ordinates in your calculations for MSD?
> > > >
> > > > Arun
> > > >
> > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani 
> > > > wrote:
> > > >
> > > > > Hi,
> > > > > I am trying to post-processing my results and calculate MSD (mean
> > > square
> > > > > displacement) but my answer is different from the MSD value that
> > > GROMACS
> > > > > calculated. I use trjconv command and use the output .gro file. I
> > tried
> > > > to
> > > > > understand the GROMACS code but I am not a good programmer. Is
> there
> > > any
> > > > > specific detail except the Einstein relation in the manual?
> > > > >
> > > > > sorry if here is not the right place to ask this question.
> > > > > Best regards.
> > > > >
> > > > > Sina Omrani.
> > > > > --
> > > > > 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-requ...@gromacs.org.
> > > > >
> > > > --
> > > > 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-requ...@gromacs.org.
> > > >
> > > --
> > > 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-requ...@gromacs.org.
> > >
> > --
> > 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-requ...@gromacs.org.
> >
> --
> 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