Re: [gmx-users] (no subject)

[Daniel Burns]

Start here: http://www.mdtutorials.com/gmx/.  An introduction to linux book
might be helpful as well if you are not already familiar with it.

Good luck!

On Thu, Apr 2, 2020 at 2:05 PM Feriel Terbeche  wrote:

> Hello!
> My name's FERIEL TERBECHE I am a genetic studant, from ALGERIA, Im
> preparing my  last study's project (master degrees), wich is about
> hemophila A and factor VIII where I have to use gromacs, but, I don't know
> how to use it even I have it on my computer and unfortunately no one here
> can help me because no one used it before.  I really need help but I don't
> know from where I'll get it, so can I have some advices. Thank you
>
> --
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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[gmx-users] (no subject)

[Feriel Terbeche]

Hello!
My name's FERIEL TERBECHE I am a genetic studant, from ALGERIA, Im preparing my 
 last study's project (master degrees), wich is about hemophila A and factor 
VIII where I have to use gromacs, but, I don't know how to use it even I have 
it on my computer and unfortunately no one here can help me because no one used 
it before.  I really need help but I don't know from where I'll get it, so can 
I have some advices. Thank you

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[gmx-users] (no subject)

[Sutanu L'Étranger]

Hi,

I've just installed GROMACS on Linux in Virtualbox. But, now I can't find
my GROMACS, please tell me how to find it.
Thank you.

I've used these commands while installing gromacs:-

sudo apt update
sudo apt upgrade
sudo apt install gcc
sudo apt install cmake
sudo apt install build-essential
sudo apt install libfftw3-dev
sudo apt install gromacs
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Re: [gmx-users] (no subject)

[Dallas Warren]

Download and use the forcefield files from the ATB server website, and then
make that you correctly point to it in your top file.

On Sat, 14 Mar. 2020, 7:32 pm FAISAL NABI,  wrote:

> Hi,
> I have been a new user and i was following the protein-ligand complex
> tutorial for MD. I have used GROMOS96 54a7 FF and to build ligand topology
> i have used ATB webserver. I did download the .itp and .pdb file from there
> and converted that to .gro file. The problem i am facing is it shows an
> error while i add ions that "Atomtype CAro not found", although i have
> added the atomtypes in the gromacs topology file still it's showing the
> same error. I request if somebody could provie me a stepwise protocol i
> could follow.
>
> Thank you
>
> --
>
> Faisal Nabi
>
> *Pre-Doctoral Fellow (CSIR-JRF)*
> C/o Professor Rizwan Hassan Khan
> Interdisciplinary Biotechnology Unit,
> Aligarh Muslim University, Aligarh, UP, INDIA.
> Email-*fn...@myamy.ac.in *
> *  faisalbioc...@gmail.com *
> Contact no. - *+91-8923713214*
> --
> 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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Re: [gmx-users] no subject

[Prasanth G, Research Scholar]

Hello Faisal,

Easiest way to do this is by navigating to the MD files tab and download
the "Gromacs 4.5.x-5.x.x 54a7" below this warning - "*Warning!* This
molecule contains non-standard atom types not included in the standard
GROMOS 54A7 forcefield..."

The folder contains the procedure to modify the 54a7 forcefield to include
the non-standard atomtypes.
However the easiest way to just include the whole folder in your working
directory (wd) and when you prepare gro from pdb in the first step, you can
choose the option 1 (you will see that you receive a prompt saying this ff
is from the wd).
Hope it helps.

If you are interested in Ligand- protein interaction studies. I would
suggest you to use Amber or Charmm ff. This is because GROMOS is a united
atom ff and an all atom ff might be better in helping you understand these
interactions. Please go through the last part of this thread -
https://www.researchgate.net/post/How_can_I_use_a_Topology_file_generated_by_an_ATB_server

If you want to use Amber ff. you can use ACPYPE which works in conjunction
with AMBER to prepare files necessary in gromacs compatible format. As
antechamber (part of AMBER) is a semi qm/mm technique the parametrization
happens faster , plus it can be done directly on your system.

All the best



-- 
Regards,
Prasanth.
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[gmx-users] (no subject)

[FAISAL NABI]

Hi,
I have been a new user and i was following the protein-ligand complex
tutorial for MD. I have used GROMOS96 54a7 FF and to build ligand topology
i have used ATB webserver. I did download the .itp and .pdb file from there
and converted that to .gro file. The problem i am facing is it shows an
error while i add ions that "Atomtype CAro not found", although i have
added the atomtypes in the gromacs topology file still it's showing the
same error. I request if somebody could provie me a stepwise protocol i
could follow.

Thank you

-- 

Faisal Nabi

*Pre-Doctoral Fellow (CSIR-JRF)*
C/o Professor Rizwan Hassan Khan
Interdisciplinary Biotechnology Unit,
Aligarh Muslim University, Aligarh, UP, INDIA.
Email-*fn...@myamy.ac.in *
*  faisalbioc...@gmail.com *
Contact no. - *+91-8923713214*
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[gmx-users] (no subject)

[Afsane Farhadi]

afsane_farh...@yahoo.com

Sent from Yahoo Mail on Android
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Re: [gmx-users] (no subject)

[shakira shukoor]

Thanks christian for the detailed description.

On Mon, Feb 17, 2020 at 8:00 PM Christian Blau  wrote:

> Hi Shakkira,
>
>
> The simulation box deformation is described by six parameters that
> describe three basis box vectors with the following
> contraints,
>
>   - the first box vector is aligned along the x-axis, with coordinates
> thus has coordinates (xx,0,0)
>
>   - the second box vector is aligned in the x-y plane with coordinates
> (yx,yy,0)
>
>   - the third box vector is free (zx,zy,zz)
>
>
> The six parameters that you give in .mdp files are in the following order
>
> xx, yy, zz, yx, zx, zy
>
>
> The corrent box is then calculated as
>
> box(t_start)+(t-t_start)*deform
>
>
> For more information have a look at the gromacs manual mdp parameter
> description:
>
> http://manual.gromacs.org/current/user-guide/mdp-options.html
>
> under non-equilibrium MD:
>
> (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
> The velocities of deformation for the box elements: a(x) b(y) c(z)
> b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
> is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
> elements are corrected for periodicity. The coordinates are
> transformed accordingly. Frozen degrees of freedom are (purposely)
> also transformed. The time ts is set to t at the first step and at
> steps at which x and v are written to trajectory to ensure exact
> restarts. Deformation can be used together with semiisotropic or
> anisotropic pressure coupling when the appropriate
> compressibilities are set to zero. The diagonal elements can be
> used to strain a solid. The off-diagonal elements can be used to
> shear a solid or a liquid.
>
>
> Best,
>
> Christian
>
> On 2020-02-16 12:12, shakira shukoor wrote:
> >Hi all
> > Can anyone help me with the DEFORM option in Gromacs to change the box
> > values?
> >
> >
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-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106
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Re: [gmx-users] (no subject)

[Christian Blau]

Hi Shakkira,


The simulation box deformation is described by six parameters that describe three basis box vectors with the following 
contraints,


 - the first box vector is aligned along the x-axis, with coordinates thus has 
coordinates (xx,0,0)

 - the second box vector is aligned in the x-y plane with coordinates (yx,yy,0)

 - the third box vector is free (zx,zy,zz)


The six parameters that you give in .mdp files are in the following order

xx, yy, zz, yx, zx, zy


The corrent box is then calculated as

box(t_start)+(t-t_start)*deform


For more information have a look at the gromacs manual mdp parameter 
description:

http://manual.gromacs.org/current/user-guide/mdp-options.html

under non-equilibrium MD:

   (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
   The velocities of deformation for the box elements: a(x) b(y) c(z)
   b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
   is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
   elements are corrected for periodicity. The coordinates are
   transformed accordingly. Frozen degrees of freedom are (purposely)
   also transformed. The time ts is set to t at the first step and at
   steps at which x and v are written to trajectory to ensure exact
   restarts. Deformation can be used together with semiisotropic or
   anisotropic pressure coupling when the appropriate
   compressibilities are set to zero. The diagonal elements can be
   used to strain a solid. The off-diagonal elements can be used to
   shear a solid or a liquid.


Best,

Christian

On 2020-02-16 12:12, shakira shukoor wrote:

   Hi all
Can anyone help me with the DEFORM option in Gromacs to change the box
values?



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[gmx-users] (no subject)

[shakira shukoor]

  Hi all
Can anyone help me with the DEFORM option in Gromacs to change the box
values?


-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 2/14/20 12:05 AM, Neha Tiwari wrote:

Dear Gromacs experts,
I have generated topology files(.itp) of the ligand from the ATB server and
everything goes well, but when it comes to generating ions.tpr file, I am
getting following error.


$ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

   :-) GROMACS - gmx grompp, 2018.1 (-:



 GROMACS is written by:

  Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C.
Berendsen

 Par BjelkmarAldert van Buuren   Rudi van Drunen Anton Feenstra

   Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca Hamuraru

  Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus


   Carsten Kutzner  Per Larsson  Justin A. LemkulViveca Lindahl

   Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu Murtola

 Szilard Pall   Sander Pronk  Roland Schulz Alexey Shvetsov

Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen

  Christian WennbergMaarten Wolf

and the project leaders:

 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel



Copyright (c) 1991-2000, University of Groningen, The Netherlands.

Copyright (c) 2001-2017, The GROMACS development team at

Uppsala University, Stockholm University and

the Royal Institute of Technology, Sweden.

check out http://www.gromacs.org for more information.



GROMACS is free software; you can redistribute it and/or modify it

under the terms of the GNU Lesser General Public License

as published by the Free Software Foundation; either version 2.1

of the License, or (at your option) any later version.



GROMACS:  gmx grompp, version 2018.1

Executable:   /usr/bin/gmx

Data prefix:  /usr

Working dir:  /home/ya/Desktop/Neha/fecA/gromos

Command line:

   gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr



Ignoring obsolete mdp entry 'title'



NOTE 1 [file ions.mdp]:

   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note

   that with the Verlet scheme, nstlist has no effect on the accuracy of

   your simulation.



Setting the LD random seed to 49113858

Generated 165 of the 1596 non-bonded parameter combinations

Excluding 3 bonded neighbours molecule type 'Protein'

Excluding 3 bonded neighbours molecule type '4JCP'

Excluding 2 bonded neighbours molecule type 'SOL'



NOTE 2 [file topol.top, line 45350]:

   System has non-zero total charge: -14.00

   Total charge should normally be an integer. See

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

   for discussion on how close it should be to an integer.







Removing all charge groups because cutoff-scheme=Verlet



ERROR 1 [file topol.top, line 45350]:

   atom O10 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 2 [file topol.top, line 45350]:

   atom C2 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 3 [file topol.top, line 45350]:

   atom O9 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 4 [file topol.top, line 45350]:

   atom Fe14 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 5 [file topol.top, line 45350]:

   atom C3 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 6 [file topol.top, line 45350]:

   atom C4 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 7 [file topol.top, line 45350]:

   atom O11 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 8 [file topol.top, line 45350]:

   atom H19 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 9 [file topol.top, line 45350]:

   atom C6 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 10 [file topol.top, line 45350]:

   atom O12 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 11 [file topol.top, line 45350]:

   atom O13 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 12 [file topol.top, line 45350]:

   atom C5 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 13 [file topol.top, line 45350]:

   atom C1 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 14 [file topol.top, line 45350]:

   atom O7 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 15 [file topol.top, line 45350]:

   atom O8 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







There were 2 notes



---

Program: gmx grompp, version 2018.1

Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2137)



Fatal error:

There were 15 errors in input file(s)



Likely the format/contents of those topology lines are wrong if grompp 
finds zero mass.


-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

[gmx-users] (no subject)

[Neha Tiwari]

Dear Gromacs experts,
I have generated topology files(.itp) of the ligand from the ATB server and
everything goes well, but when it comes to generating ions.tpr file, I am
getting following error.


$ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

  :-) GROMACS - gmx grompp, 2018.1 (-:



GROMACS is written by:

 Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C.
Berendsen

Par BjelkmarAldert van Buuren   Rudi van Drunen Anton Feenstra

  Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca Hamuraru

 Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus


  Carsten Kutzner  Per Larsson  Justin A. LemkulViveca Lindahl

  Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu Murtola

Szilard Pall   Sander Pronk  Roland Schulz Alexey Shvetsov

   Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen

 Christian WennbergMaarten Wolf

   and the project leaders:

Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel



Copyright (c) 1991-2000, University of Groningen, The Netherlands.

Copyright (c) 2001-2017, The GROMACS development team at

Uppsala University, Stockholm University and

the Royal Institute of Technology, Sweden.

check out http://www.gromacs.org for more information.



GROMACS is free software; you can redistribute it and/or modify it

under the terms of the GNU Lesser General Public License

as published by the Free Software Foundation; either version 2.1

of the License, or (at your option) any later version.



GROMACS:  gmx grompp, version 2018.1

Executable:   /usr/bin/gmx

Data prefix:  /usr

Working dir:  /home/ya/Desktop/Neha/fecA/gromos

Command line:

  gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr



Ignoring obsolete mdp entry 'title'



NOTE 1 [file ions.mdp]:

  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note

  that with the Verlet scheme, nstlist has no effect on the accuracy of

  your simulation.



Setting the LD random seed to 49113858

Generated 165 of the 1596 non-bonded parameter combinations

Excluding 3 bonded neighbours molecule type 'Protein'

Excluding 3 bonded neighbours molecule type '4JCP'

Excluding 2 bonded neighbours molecule type 'SOL'



NOTE 2 [file topol.top, line 45350]:

  System has non-zero total charge: -14.00

  Total charge should normally be an integer. See

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

  for discussion on how close it should be to an integer.







Removing all charge groups because cutoff-scheme=Verlet



ERROR 1 [file topol.top, line 45350]:

  atom O10 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 2 [file topol.top, line 45350]:

  atom C2 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 3 [file topol.top, line 45350]:

  atom O9 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 4 [file topol.top, line 45350]:

  atom Fe14 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 5 [file topol.top, line 45350]:

  atom C3 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 6 [file topol.top, line 45350]:

  atom C4 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 7 [file topol.top, line 45350]:

  atom O11 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 8 [file topol.top, line 45350]:

  atom H19 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 9 [file topol.top, line 45350]:

  atom C6 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 10 [file topol.top, line 45350]:

  atom O12 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 11 [file topol.top, line 45350]:

  atom O13 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 12 [file topol.top, line 45350]:

  atom C5 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 13 [file topol.top, line 45350]:

  atom C1 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 14 [file topol.top, line 45350]:

  atom O7 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 15 [file topol.top, line 45350]:

  atom O8 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







There were 2 notes



---

Program: gmx grompp, version 2018.1

Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2137)



Fatal error:

There were 15 errors in input file(s)



For more information and tips for troubleshooting, please check the GROMACS

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




Please help.
Thanks in advance.

Regards,
Neha.
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Re: [gmx-users] (no subject)

[Quyen V. Vu]

for what reasons you request the largest force in your system smaller than
such small value?

On Fri, Jan 24, 2020 at 1:22 PM Sadaf Rani  wrote:

> Dear Gromacs users
> I am running a free energy calculation of the protein-ligand complex.
> During the energy minimization process, I am getting many jumps in steps as
> below:-
>
> Step   Time
>   1050010500.0
>
>Energies (kJ/mol)
>Bond Restraint Pot.  AngleProper Dih.  Improper Dih.
> 1.20860e+031.65864e+004.67218e+031.83350e+041.87873e+02
>   LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
> 6.81295e+037.12692e+043.37954e+05   -6.56537e+03   -2.70668e+06
>Coul. recip.Angle Rest. Dih. Rest.  Potential Pres. DC (bar)
> 4.78029e+035.32468e+003.32764e+00   -2.26802e+060.0e+00
>  Pressure (bar)dVremain/dl   dEkin/dl  dVcoul/dl   dVvdw/dl
>-2.69428e+040.0e+000.0e+002.78529e+03   -1.65404e+02
>  dVrestraint/dl   Constr. rmsd
> 0.0e+002.71623e-06
>
>Step   Time
>   1050110501.0
>
>Step   Time
>   1050210502.0
>
>Step   Time
>   1050310503.0
>
>Step   Time
>   1050410504.0
>
>Step   Time
>   1050510505.0
>
>Step   Time
>   1050610506.0
>
>Step   Time
>   1050710507.0
>
>Step   Time
>   1050810508.0
>
>Step   Time
>   1050910509.0
>
>Step   Time
>   1051010510.0
>
>Step   Time
>   1051110511.0
>
>
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 10 (which may not be possible for your system).
> It
> stopped because the algorithm tried to make a new step whose size was too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> Steepest Descents converged to machine precision in 10512 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -2.2680185e+06
> Maximum force =  6.3521606e+02 on atom 4653
> Norm of force =  3.6713926e+00
>
> Should I use double precision for energy minimization?
> I need your suggestions,
>  please.
>
> Thanks
>
> Sadaf Rani
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[gmx-users] (no subject)

[Sadaf Rani]

Dear Gromacs users
I am running a free energy calculation of the protein-ligand complex.
During the energy minimization process, I am getting many jumps in steps as
below:-

Step   Time
  1050010500.0

   Energies (kJ/mol)
   Bond Restraint Pot.  AngleProper Dih.  Improper Dih.
1.20860e+031.65864e+004.67218e+031.83350e+041.87873e+02
  LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
6.81295e+037.12692e+043.37954e+05   -6.56537e+03   -2.70668e+06
   Coul. recip.Angle Rest. Dih. Rest.  Potential Pres. DC (bar)
4.78029e+035.32468e+003.32764e+00   -2.26802e+060.0e+00
 Pressure (bar)dVremain/dl   dEkin/dl  dVcoul/dl   dVvdw/dl
   -2.69428e+040.0e+000.0e+002.78529e+03   -1.65404e+02
 dVrestraint/dl   Constr. rmsd
0.0e+002.71623e-06

   Step   Time
  1050110501.0

   Step   Time
  1050210502.0

   Step   Time
  1050310503.0

   Step   Time
  1050410504.0

   Step   Time
  1050510505.0

   Step   Time
  1050610506.0

   Step   Time
  1050710507.0

   Step   Time
  1050810508.0

   Step   Time
  1050910509.0

   Step   Time
  1051010510.0

   Step   Time
  1051110511.0


Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 10 (which may not be possible for your system).
It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

Steepest Descents converged to machine precision in 10512 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -2.2680185e+06
Maximum force =  6.3521606e+02 on atom 4653
Norm of force =  3.6713926e+00

Should I use double precision for energy minimization?
I need your suggestions,
 please.

Thanks

Sadaf Rani
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 12/25/19 11:14 PM, Najamuddin Memon wrote:

It is not about to select numbers in drop down menu. You should write atom
no of protein and ligand. For example your chain a is protein having 2000
atoms. The atom no starts from 1 till 2000 for protein. And for chain b is
your ligand and your ligand has 40 atoms it is from 2001 till 2040. You can
see these atom no in .top file.


More easily, one can identify which residues reside in loops and simply 
select by residue by using make_ndx.


-Justin


On Wed, Dec 25, 2019, 8:54 PM nupur munjal  wrote:


Hi,
i am trying to make the index file without loops and termini and using the
option protein and ligand that is 1 and 13 but the index file is formed
with the same as it is formed from the whole system.

--
Kind Regards
Nupur Munjal
PhD Scholar (Bioinformatics)
Department of Biotechnology & Bioinformatics
Jaypee University of Information Technology
Waknaghat, Solan,India

The only thing that overcomes hard luck is hard work - Harry Golden

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==

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Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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==

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Re: [gmx-users] (no subject)

[Najamuddin Memon]

It is not about to select numbers in drop down menu. You should write atom
no of protein and ligand. For example your chain a is protein having 2000
atoms. The atom no starts from 1 till 2000 for protein. And for chain b is
your ligand and your ligand has 40 atoms it is from 2001 till 2040. You can
see these atom no in .top file.

On Wed, Dec 25, 2019, 8:54 PM nupur munjal  wrote:

> Hi,
> i am trying to make the index file without loops and termini and using the
> option protein and ligand that is 1 and 13 but the index file is formed
> with the same as it is formed from the whole system.
>
> --
> Kind Regards
> Nupur Munjal
> PhD Scholar (Bioinformatics)
> Department of Biotechnology & Bioinformatics
> Jaypee University of Information Technology
> Waknaghat, Solan,India
>
> The only thing that overcomes hard luck is hard work - Harry Golden
>
> [image: Mailtrack]
> <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> Sender
> notified by
> Mailtrack
> <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> 12/25/19,
> 9:22:30 PM
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[gmx-users] (no subject)

[nupur munjal]

Hi,
i am trying to make the index file without loops and termini and using the
option protein and ligand that is 1 and 13 but the index file is formed
with the same as it is formed from the whole system.

-- 
Kind Regards
Nupur Munjal
PhD Scholar (Bioinformatics)
Department of Biotechnology & Bioinformatics
Jaypee University of Information Technology
Waknaghat, Solan,India

The only thing that overcomes hard luck is hard work - Harry Golden

[image: Mailtrack]

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9:22:30 PM
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[gmx-users] (no subject)

[Emran Heshmati]

Dear All
I am in trouble with gmx distance command. I want to calculate the distance
between two amino acids (residue 130 and residue 153) in a protein after
gromacs standard simulation. After generating of r130.ndx and r153.ndx
index files, I use this command:
gmx distance -f md_0_1_noPBC.xtc -s md_0_1.tpr -oav distave.xvg -oall
dist.xvg -oh disthist.xvg -b 7 -e 10
but don't list r130 and r153 as extra groups. Adding -n *.ndx option
didn't  sole the problem. Any comment please.
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Re: [gmx-users] (no subject)

[shakuntala dhurua]

Ok i will try, thank you so much

On Mon, 9 Dec 2019, 1:07 pm Tasneem Kausar, 
wrote:

> This problem also occurs in gromacs-5.1.4. Try higher version. We have done
> these calculations on gromacs-2016.
>
> On Mon, Dec 9, 2019 at 10:49 AM shakuntala dhurua <
> madhu.dhuru...@gmail.com>
> wrote:
>
> > here I am using gromacs version --- gromacs-5.1.5
> >
> > On Mon, Dec 9, 2019 at 10:43 AM Tasneem Kausar <
> tasneemkausa...@gmail.com>
> > wrote:
> >
> > > Please specify your gromacs version.
> > >
> > > On Mon, Dec 9, 2019 at 10:04 AM shakuntala dhurua <
> > > madhu.dhuru...@gmail.com>
> > > wrote:
> > >
> > > > hi
> > > > I am facing problem during hydrogen bond correlation c(t) with error
> > > > segmentation fault
> > > > I have used following flag for generate xtc file::- gmx trjconv -n
> > > > index.ndx -s ins_prod_1.tpr -f ins_prod_1.trr -o ins_prod_1.xtc -pbc
> > > > cluster
> > > > then for hydrogen bond correlation used following flag ::-gmx hbond
> -n
> > > > index.ndx -s ins_prod_1.tpr -f ins_prod_1.xtc -ac ins_prod_1.xvg
> > > > following error I am getting
> > > > Doing autocorrelation according to the theory of Luzar and Chandler.
> > > > Segmentation fault (core dumped)
> > > > please suggest me to solve this problem
> > > > --
> > > > Gromacs Users mailing list
> > > >
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> > > > posting!
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> or
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> > > >
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Re: [gmx-users] (no subject)

[shakuntala dhurua]

here I am using gromacs version --- gromacs-5.1.5

On Mon, Dec 9, 2019 at 10:43 AM Tasneem Kausar 
wrote:

> Please specify your gromacs version.
>
> On Mon, Dec 9, 2019 at 10:04 AM shakuntala dhurua <
> madhu.dhuru...@gmail.com>
> wrote:
>
> > hi
> > I am facing problem during hydrogen bond correlation c(t) with error
> > segmentation fault
> > I have used following flag for generate xtc file::- gmx trjconv -n
> > index.ndx -s ins_prod_1.tpr -f ins_prod_1.trr -o ins_prod_1.xtc -pbc
> > cluster
> > then for hydrogen bond correlation used following flag ::-gmx hbond -n
> > index.ndx -s ins_prod_1.tpr -f ins_prod_1.xtc -ac ins_prod_1.xvg
> > following error I am getting
> > Doing autocorrelation according to the theory of Luzar and Chandler.
> > Segmentation fault (core dumped)
> > please suggest me to solve this problem
> > --
> > Gromacs Users mailing list
> >
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> > posting!
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> >
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Re: [gmx-users] (no subject)

[Tasneem Kausar]

Please specify your gromacs version.

On Mon, Dec 9, 2019 at 10:04 AM shakuntala dhurua 
wrote:

> hi
> I am facing problem during hydrogen bond correlation c(t) with error
> segmentation fault
> I have used following flag for generate xtc file::- gmx trjconv -n
> index.ndx -s ins_prod_1.tpr -f ins_prod_1.trr -o ins_prod_1.xtc -pbc
> cluster
> then for hydrogen bond correlation used following flag ::-gmx hbond -n
> index.ndx -s ins_prod_1.tpr -f ins_prod_1.xtc -ac ins_prod_1.xvg
> following error I am getting
> Doing autocorrelation according to the theory of Luzar and Chandler.
> Segmentation fault (core dumped)
> please suggest me to solve this problem
> --
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[gmx-users] (no subject)

[shakuntala dhurua]

hi
I am facing problem during hydrogen bond correlation c(t) with error
segmentation fault
I have used following flag for generate xtc file::- gmx trjconv -n
index.ndx -s ins_prod_1.tpr -f ins_prod_1.trr -o ins_prod_1.xtc -pbc cluster
then for hydrogen bond correlation used following flag ::-gmx hbond -n
index.ndx -s ins_prod_1.tpr -f ins_prod_1.xtc -ac ins_prod_1.xvg
following error I am getting
Doing autocorrelation according to the theory of Luzar and Chandler.
Segmentation fault (core dumped)
please suggest me to solve this problem
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 11/19/19 5:55 AM, Bratin Kumar Das wrote:

Hi
 I hope there is a problem in the topology...please follow the gromacs
tutorial..


More specifically: http://www.mdtutorials.com/gmx/complex/index.html

The #include statements are out of order. You cannot add new parameters 
to the topology after any [moleculetype] has been declared. The entire 
force field must be known before any species can be introduced.


-Justin


On Tue 19 Nov, 2019, 3:34 PM Alessandra Villa, <
alessandra.villa.bio...@gmail.com> wrote:


Hi,
Pls note that the maillist does not support attachments.
Also it will better/helpful to use emails subject.
Kind regards
Alessandra

On Tue, Nov 19, 2019 at 10:46 AM pooja kesari 
wrote:


Dear All,
I am doing a protein-ligand simulation, when i was try to *add ions to

the

system*
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
*there was an error*
Fatal error:
Syntax error - File lig.prm, line 2
Last line read:
'[ bondtypes ]'
Invalid order for directive bondtypes
*my topol.top- ligand defination is as follows *
  ; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include ligand parameters
#include "lig.prm"

; Include ligand topology
#include "lig.itp"

; Include water topology
#include "./charmm36-mar2019.ff/tip3p.itp"

I have included the ligand parameter details as suggested in lig.top file
generated by cgenff python script. I have attached the itp and prm file

for

reference.



Thanks & Regards,
Dr. Pooja Kesari
Post Doctoral Fellow
Department Of Biosciences and Bioengineering
Indian Institute of Technology Bombay
INDIA
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--
==

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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

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Re: [gmx-users] (no subject)

[Bratin Kumar Das]

Hi
I hope there is a problem in the topology...please follow the gromacs
tutorial..

On Tue 19 Nov, 2019, 3:34 PM Alessandra Villa, <
alessandra.villa.bio...@gmail.com> wrote:

> Hi,
> Pls note that the maillist does not support attachments.
> Also it will better/helpful to use emails subject.
> Kind regards
> Alessandra
>
> On Tue, Nov 19, 2019 at 10:46 AM pooja kesari 
> wrote:
>
> > Dear All,
> > I am doing a protein-ligand simulation, when i was try to *add ions to
> the
> > system*
> > gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
> > *there was an error*
> > Fatal error:
> > Syntax error - File lig.prm, line 2
> > Last line read:
> > '[ bondtypes ]'
> > Invalid order for directive bondtypes
> > *my topol.top- ligand defination is as follows *
> >  ; Include Position restraint file
> > #ifdef POSRES
> > #include "posre.itp"
> > #endif
> >
> > ; Include ligand parameters
> > #include "lig.prm"
> >
> > ; Include ligand topology
> > #include "lig.itp"
> >
> > ; Include water topology
> > #include "./charmm36-mar2019.ff/tip3p.itp"
> >
> > I have included the ligand parameter details as suggested in lig.top file
> > generated by cgenff python script. I have attached the itp and prm file
> for
> > reference.
> >
> >
> >
> > Thanks & Regards,
> > Dr. Pooja Kesari
> > Post Doctoral Fellow
> > Department Of Biosciences and Bioengineering
> > Indian Institute of Technology Bombay
> > INDIA
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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> > posting!
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Re: [gmx-users] (no subject)

[Alessandra Villa]

Hi,
Pls note that the maillist does not support attachments.
Also it will better/helpful to use emails subject.
Kind regards
Alessandra

On Tue, Nov 19, 2019 at 10:46 AM pooja kesari 
wrote:

> Dear All,
> I am doing a protein-ligand simulation, when i was try to *add ions to the
> system*
> gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
> *there was an error*
> Fatal error:
> Syntax error - File lig.prm, line 2
> Last line read:
> '[ bondtypes ]'
> Invalid order for directive bondtypes
> *my topol.top- ligand defination is as follows *
>  ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include ligand parameters
> #include "lig.prm"
>
> ; Include ligand topology
> #include "lig.itp"
>
> ; Include water topology
> #include "./charmm36-mar2019.ff/tip3p.itp"
>
> I have included the ligand parameter details as suggested in lig.top file
> generated by cgenff python script. I have attached the itp and prm file for
> reference.
>
>
>
> Thanks & Regards,
> Dr. Pooja Kesari
> Post Doctoral Fellow
> Department Of Biosciences and Bioengineering
> Indian Institute of Technology Bombay
> INDIA
> --
> 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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[gmx-users] (no subject)

[pooja kesari]

Dear All,
I am doing a protein-ligand simulation, when i was try to *add ions to the
system*
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
*there was an error*
Fatal error:
Syntax error - File lig.prm, line 2
Last line read:
'[ bondtypes ]'
Invalid order for directive bondtypes
*my topol.top- ligand defination is as follows *
 ; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include ligand parameters
#include "lig.prm"

; Include ligand topology
#include "lig.itp"

; Include water topology
#include "./charmm36-mar2019.ff/tip3p.itp"

I have included the ligand parameter details as suggested in lig.top file
generated by cgenff python script. I have attached the itp and prm file for
reference.



Thanks & Regards,
Dr. Pooja Kesari
Post Doctoral Fellow
Department Of Biosciences and Bioengineering
Indian Institute of Technology Bombay
INDIA
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[gmx-users] (no subject)

[Yogesh Sharma]

greetings everyone

I was following protein ligand complex tutorial.

EM run was fine even with double precision.

Steepest Descents converged to Fmax < 1000 in 101 steps
Potential Energy  = -2.71399964872904e+06
Maximum force =  9.15885947946535e+02 on atom 4411
Norm of force =  1.98296351352040e+01

But when I proceeded to nvt or npt equlibriation run. I am getting

starting mdrun 'SOL'
5 steps,100.0 ps.
 segmental fault core dumped.

To troubleshoot I checked .gro file for atom 4411.

459TRPNE1 4411   5.806   5.696   4.267

33678SOL OW 4411   5.925  11.717   8.738

I am attaching picture here for 4411 atom containing residues for reference.

Both of the atoms are inside box parameters.

 I even decreased temperature to 1K  or  30K but all in vain

Can you help me with this? Thank you.
 *  with  regards*
*Yogesh Sharma*
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Re: [gmx-users] (no subject)

[shakuntala dhurua]

thanks Prof. Justin

On Tue, Nov 12, 2019 at 8:48 PM Justin Lemkul  wrote:

>
> Please use an appropriate subject line.
>
> On 11/12/19 5:29 AM, shakuntala dhurua wrote:
> > hello,
> > Here I want to generate arg.pdb to arg.gro by using amber99sb force
> field .
> > for test i have used 1 residue of arginine but i got Fatal error:
> > There is a dangling bond at at least one of the terminal ends and the
> force
> > field does not provide terminal entries or files. Fix your terminal
> > residues so that they match the residue database (.rtp) entries, or
> provide
> > terminal database entries (.tdb). and following is the attach pdb format
> > which i have used for pdb2gmx ,please suggest me to solve this problem
>
> AMBER does not support zwitterionic forms of single amino acids, at
> least not within GROMACS. There may be a way to create such residues
> from the AMBER parameter database, but you'll have to look into
> published works on their force field parametrization to see if such
> residue definitions exist.
>
> -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
>
> ==
>
> --
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Re: [gmx-users] (no subject)

[shakuntala dhurua]

thanks Bratin for your suggestion

On Tue, 12 Nov 2019, 7:54 pm Bratin Kumar Das, <177cy500.bra...@nitk.edu.in>
wrote:

> I think you have capped your residue in the N-terminal and C-terminal
> end...and the capping is not defined in your .rtp entry.. that's why this
> error is coming
>
> On Tue 12 Nov, 2019, 3:58 PM shakuntala dhurua, 
> wrote:
>
> > hello,
> > Here I want to generate arg.pdb to arg.gro by using amber99sb force
> field .
> > for test i have used 1 residue of arginine but i got Fatal error:
> > There is a dangling bond at at least one of the terminal ends and the
> force
> > field does not provide terminal entries or files. Fix your terminal
> > residues so that they match the residue database (.rtp) entries, or
> provide
> > terminal database entries (.tdb). and following is the attach pdb format
> > which i have used for pdb2gmx ,please suggest me to solve this problem
> > --
> > 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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Re: [gmx-users] (no subject)

[Justin Lemkul]

Please use an appropriate subject line.

On 11/12/19 5:29 AM, shakuntala dhurua wrote:

hello,
Here I want to generate arg.pdb to arg.gro by using amber99sb force field .
for test i have used 1 residue of arginine but i got Fatal error:
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Fix your terminal
residues so that they match the residue database (.rtp) entries, or provide
terminal database entries (.tdb). and following is the attach pdb format
which i have used for pdb2gmx ,please suggest me to solve this problem


AMBER does not support zwitterionic forms of single amino acids, at 
least not within GROMACS. There may be a way to create such residues 
from the AMBER parameter database, but you'll have to look into 
published works on their force field parametrization to see if such 
residue definitions exist.


-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

==

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Re: [gmx-users] (no subject)

[Bratin Kumar Das]

I think you have capped your residue in the N-terminal and C-terminal
end...and the capping is not defined in your .rtp entry.. that's why this
error is coming

On Tue 12 Nov, 2019, 3:58 PM shakuntala dhurua, 
wrote:

> hello,
> Here I want to generate arg.pdb to arg.gro by using amber99sb force field .
> for test i have used 1 residue of arginine but i got Fatal error:
> There is a dangling bond at at least one of the terminal ends and the force
> field does not provide terminal entries or files. Fix your terminal
> residues so that they match the residue database (.rtp) entries, or provide
> terminal database entries (.tdb). and following is the attach pdb format
> which i have used for pdb2gmx ,please suggest me to solve this problem
> --
> 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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[gmx-users] (no subject)

[shakuntala dhurua]

hello,
Here I want to generate arg.pdb to arg.gro by using amber99sb force field .
for test i have used 1 residue of arginine but i got Fatal error:
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Fix your terminal
residues so that they match the residue database (.rtp) entries, or provide
terminal database entries (.tdb). and following is the attach pdb format
which i have used for pdb2gmx ,please suggest me to solve this problem
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Re: [gmx-users] (no subject)

[shakuntala dhurua]

Thank you sir for your suggestions

On Fri, 8 Nov 2019, 7:31 pm Christian Blau,  wrote:

> Hello Shakuntala,
>
>
> If you already have the trajectories, you have to post-process at least
> once to filter the data down to a manageable
> size, and once to do the periodic boundary condition fix precisely as you
> described.
>
> If you set up a new simulation you may use "nstxout-compressed" to control
> the output frequency for your xtc file. It is
> very unlikely that you will need a .trr file, so you can even set nstxout,
> nstvout and nstfout to zero. Starting your
> post-processing from a xtc should speed up your analysis process.
>
>
> On another note: Please fill in a subject line in your emails, it makes it
> easier to search and keep track of the
> ongoing discussions.
>
>
> Best,
>
> Christian
>
>
> On 11/7/19 3:12 PM, shakuntala dhurua wrote:
> > I would like to calculate rmsd of protein system, but there is much time
> > taking for trjcat of all simulated trajectories (.trr file) then
> generated
> > .xtc file by using -center -pbc mol flag. from this .xtc file i use to
> > calculate rms value by using flag g_rms -f .xtc -s .tpr -n .ndx -o .xvg I
> > want to ask here is any other way is available to directly calculate rmsd
> > without using trjcat or less time taking method.
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Re: [gmx-users] (no subject)

[Christian Blau]

Hello Shakuntala,


If you already have the trajectories, you have to post-process at least once to filter the data down to a manageable 
size, and once to do the periodic boundary condition fix precisely as you described.


If you set up a new simulation you may use "nstxout-compressed" to control the output frequency for your xtc file. It is 
very unlikely that you will need a .trr file, so you can even set nstxout, nstvout and nstfout to zero. Starting your 
post-processing from a xtc should speed up your analysis process.



On another note: Please fill in a subject line in your emails, it makes it easier to search and keep track of the 
ongoing discussions.



Best,

Christian


On 11/7/19 3:12 PM, shakuntala dhurua wrote:

I would like to calculate rmsd of protein system, but there is much time
taking for trjcat of all simulated trajectories (.trr file) then generated
.xtc file by using -center -pbc mol flag. from this .xtc file i use to
calculate rms value by using flag g_rms -f .xtc -s .tpr -n .ndx -o .xvg I
want to ask here is any other way is available to directly calculate rmsd
without using trjcat or less time taking method.

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[gmx-users] (no subject)

[shakuntala dhurua]

I would like to calculate rmsd of protein system, but there is much time
taking for trjcat of all simulated trajectories (.trr file) then generated
.xtc file by using -center -pbc mol flag. from this .xtc file i use to
calculate rms value by using flag g_rms -f .xtc -s .tpr -n .ndx -o .xvg I
want to ask here is any other way is available to directly calculate rmsd
without using trjcat or less time taking method.
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[gmx-users] (no subject)

[Ayesha Kanwal]

Hi all,
i am preparing system of DNA-protein complex, downloaded it from RCSB website, 
by using GROMACS force field AMBER03WS with water Model TIP4P (2005). The DNA 
chain contains DA, DT, DG, DC atom type.
but the problem is that when i use command for energy minimization the 
following error has occurred. Error shows that problem is in .itp file Dih. 
types. Its my first time i am preparing this kind of system please let me know 
how can i resolve this problem and why this error generated ? I have searched 
out previous mail but could not find relevant answer so i am posting it now 
here. i have attached .mdp file with this e-mail.

checking input for internal consistency...
Generated 2412 of the 2415 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2415 of the 2415 1-4 parameter combinations

ERROR 1 [file dna-his_DNA_chain_I.itp, line 44148]:
  No default Improper Dih. types


ERROR 2 [file dna-his_DNA_chain_J.itp, line 44148]:
  No default Improper Dih. types

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Re: [gmx-users] (no subject)

[Christian Blau]

Hello Saranya,

Now again with readable formatting. Also note that it is very useful to people 
on gmx-useres to  specify the subject when writing emails, because it makes it 
easier to search, reply, and handle multiple discussion threads.

This error means that during the nvt equilibrium high forces occurred that made 
it impossible to resolve the bond constraints. The very high forces occurred 
most likely are due to some high tension in the system.

As indicated in the error message you can:
 - Reduce the time step of your run initially to relax the structure first.
 - Check the output PDB structure at the site where the error occurred (atoms 
217 and 218), possibly removing or displacing the offending water molecule 
manually
 - Check that you used a well relaxed structure from energy minimisation

Best,
Christian

On 11/1/19 7:48 AM, saranya wrote:

Hello everyone,
while running nvt equilibration i am getting the error as:
Step 12, time 0.024 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 92522.640625 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 277278   58.90.1090  74.2482  0.1090
 281282   35.80.1098  73.5336  0.1090
 281283  119.30.1097  74.0780  0.1090
 281284   63.50.1097  74.2253  0.1090

step 12: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step12b.pdb to ./#step12b.pdb.1#

Back Off! I just backed up step12c.pdb to ./#step12c.pdb.1#
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)



how can i resolve this error...?

With Regards,

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*

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Re: [gmx-users] (no subject)

[blau]

Hello Saranya,This error means that during the nvt equilibrium high forces 
occurred that made it impossible to resolve the bond constraints. The very high 
forces occurred most likely are due to some high tension in the system. As 
indicated in the error message you can. Reduce the time step of your run 
initially to relax the structure first. Check the output PDB structure at the 
site where the error occurred (atoms 217 and 218), possibly removing or 
displacing the offending water molecule manually. Check that you used a well 
relaxed structure from energy minimisationBest, Christian
 Original message From: saranya  
Date: 01/11/2019  07:48  (GMT+01:00) To: gmx-us...@gromacs.org Subject: 
[gmx-users] (no subject) Hello everyone,while running nvt equilibration i am 
getting the error as:Step 12, time 0.024 (ps)  LINCS WARNINGrelative constraint 
deviation after LINCS:rms nan, max 92522.640625 (between atoms 217 and 
218)bonds that rotated more than 30 degrees: atom 1 atom 2  angle  previous, 
current, constraint length    277    278   58.9    0.1090  74.2482  0.1090  
  281    282   35.8    0.1098  73.5336  0.1090    281    283  119.3    
0.1097  74.0780  0.1090    281    284   63.5    0.1097  74.2253  
0.1090step 12: One or more water molecules can not be settled.Check for bad 
contacts and/or reduce the timestep if appropriate.Back Off! I just backed up 
step12b.pdb to ./#step12b.pdb.1#Back Off! I just backed up step12c.pdb to 
./#step12c.pdb.1#Wrote pdb files with previous and current 
coordinatesSegmentation fault (core dumped)how can i resolve this error...?With 
Regards,*Saranya Vasudevan,**Research Scholar,**Molecular Quantum Mechanics 
Laboratory,**Department of Physics,**Bharathiar University,**Coimbatore-46*-- 
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[gmx-users] (no subject)

[saranya]

Hello everyone,
while running nvt equilibration i am getting the error as:
Step 12, time 0.024 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 92522.640625 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
277278   58.90.1090  74.2482  0.1090
281282   35.80.1098  73.5336  0.1090
281283  119.30.1097  74.0780  0.1090
281284   63.50.1097  74.2253  0.1090

step 12: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step12b.pdb to ./#step12b.pdb.1#

Back Off! I just backed up step12c.pdb to ./#step12c.pdb.1#
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)



how can i resolve this error...?

With Regards,

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*
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Re: [gmx-users] (no subject)

[Dallas Warren]

Look in, or search the archive, the responses are there.

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/

On Mon, 30 Sep. 2019, 1:02 am Mahsa Rezaei, 
wrote:

> Dear gromacs users,
>
> Sorry for repeating my question.
>
> I didn't receive any email so I couldn't reply and I missed
>
>  them.
>
> I am using following pull code in md simulation
> for pulling a ligand across the plasma membrane model.
> Ligand passes through the membrane,but along simulation,
> the size of axis z increases.
> My size box is 8.52807   8.52807  14.0.
> And the pull distance is less than one-half the length of the box vector
> along.pull distance is 6 nm.
> After simulation my size box is 8.09025   8.09025  91.84508.
>
> I made my protein-membrane system with charmm-gui.
>
> so my force is charmm36.
>
> I used the equilibration input files that charmm-gui provide ,
>
> and run 400 ns simulation for equilibration of my system .
>
> RMSD , temperature and pressure is good , so I think my system is stable .
>
> Every thing is good until I use following pull code in my mdp file .
>
> The bilayer does not move and the ligand passes through the membrane
>
> But over time , the length of the z axis increases , and
>
> 4 water molecules are also separated from the membrane.
>
> What should I do?
>
> I would be very appreciated for your such kind helps.
>
> My mdp file  :
> title   = Umbrella pulling simulation
> ; Run parameters
> integrator  = md
> dt  = 0.002
> tinit   = 0
> nsteps  = 30 ; 600 ps
>
> ; Output parameters
> nstlog  = 1000
> nstxout = 500   ; every 1 ps
> nstvout = 500
> nstfout = 500
> nstxtcout   = 500; every 1 ps
> nstcalcenergy   = 500
> nstenergy   = 500
> ; PME electrostatics parameters
> coulombtype = pme
> ; Single-range cutoff scheme
> cutoff-scheme   = Verlet
> nstlist = 20
> rlist   = 1.2
> rcoulomb= 1.2
> vdwtype = Cut-off
> vdw-modifier= Force-switch
> rvdw_switch = 1.0
> rvdw= 1.2
> ; Berendsen tempearture coupling is on in two groups
> tcoupl  = nose-hoover
> tc_grps = Protein_LIG TIP3_CLA DOPC
> tau_t   = 1.01.0   1.0
> ref_t   = 303.15 303.15 303.15
> ; Pressure coupling is on
> pcoupl  = Parrinello-Rahman
> pcoupltype  = semiisotropic
> tau_p   = 5.0
> compressibility = 4.5e-5  4.5e-5
> ref_p   = 1.0 1.0
> refcoord_scaling= com
> ; Bond parameters
> constraints = h-bonds
> constraint_algorithm= LINCS
> continuation= yes
> ;
> nstcomm = 100
> comm_mode   = linear
> comm_grps   = Protein_LIG TIP3_CLA DOPC
> ; Generate velocities is off
> gen_vel = no
> ; Periodic boundary conditions are on in all directions
> pbc = xyz
>
> ; Pull code
> pull= yes
> pull_ncoords= 1 ; only one reaction coordinate
> pull_ngroups= 2 ; two groups defining one reaction
> coordinate
> pull_group1_name= BILAYER
> pull_group2_name= LIG
> pull_coord1_type= umbrella  ; harmonic potential
> pull_coord1_geometry= direction
> pull_coord1_vec = 0 0 1
> pull_coord1_groups  = 1 2
> pull_coord1_start   = yes   ; define initial COM distance > 0
> pull_coord1_rate= 0.01  ; 0.01 nm per ps =10nm per ns
> pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
> pull_nstxout= 500; every 1 ps
> pull_nstfout= 500; every 1 ps
>
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> >
> Sender
> notified by
> Mailtrack
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> 06:30:36 PM
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[gmx-users] (no subject)

[Mahsa Rezaei]

Dear gromacs users,

Sorry for repeating my question.

I didn't receive any email so I couldn't reply and I missed

 them.

I am using following pull code in md simulation
for pulling a ligand across the plasma membrane model.
Ligand passes through the membrane,but along simulation,
the size of axis z increases.
My size box is 8.52807   8.52807  14.0.
And the pull distance is less than one-half the length of the box vector
along.pull distance is 6 nm.
After simulation my size box is 8.09025   8.09025  91.84508.

I made my protein-membrane system with charmm-gui.

so my force is charmm36.

I used the equilibration input files that charmm-gui provide ,

and run 400 ns simulation for equilibration of my system .

RMSD , temperature and pressure is good , so I think my system is stable .

Every thing is good until I use following pull code in my mdp file .

The bilayer does not move and the ligand passes through the membrane

But over time , the length of the z axis increases , and

4 water molecules are also separated from the membrane.

What should I do?

I would be very appreciated for your such kind helps.

My mdp file  :
title   = Umbrella pulling simulation
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 30 ; 600 ps

; Output parameters
nstlog  = 1000
nstxout = 500   ; every 1 ps
nstvout = 500
nstfout = 500
nstxtcout   = 500; every 1 ps
nstcalcenergy   = 500
nstenergy   = 500
; PME electrostatics parameters
coulombtype = pme
; Single-range cutoff scheme
cutoff-scheme   = Verlet
nstlist = 20
rlist   = 1.2
rcoulomb= 1.2
vdwtype = Cut-off
vdw-modifier= Force-switch
rvdw_switch = 1.0
rvdw= 1.2
; Berendsen tempearture coupling is on in two groups
tcoupl  = nose-hoover
tc_grps = Protein_LIG TIP3_CLA DOPC
tau_t   = 1.01.0   1.0
ref_t   = 303.15 303.15 303.15
; Pressure coupling is on
pcoupl  = Parrinello-Rahman
pcoupltype  = semiisotropic
tau_p   = 5.0
compressibility = 4.5e-5  4.5e-5
ref_p   = 1.0 1.0
refcoord_scaling= com
; Bond parameters
constraints = h-bonds
constraint_algorithm= LINCS
continuation= yes
;
nstcomm = 100
comm_mode   = linear
comm_grps   = Protein_LIG TIP3_CLA DOPC
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz

; Pull code
pull= yes
pull_ncoords= 1 ; only one reaction coordinate
pull_ngroups= 2 ; two groups defining one reaction
coordinate
pull_group1_name= BILAYER
pull_group2_name= LIG
pull_coord1_type= umbrella  ; harmonic potential
pull_coord1_geometry= direction
pull_coord1_vec = 0 0 1
pull_coord1_groups  = 1 2
pull_coord1_start   = yes   ; define initial COM distance > 0
pull_coord1_rate= 0.01  ; 0.01 nm per ps =10nm per ns
pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
pull_nstxout= 500; every 1 ps
pull_nstfout= 500; every 1 ps

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[gmx-users] (no subject)

[Elham Zaroorati]

Hi
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Re: [gmx-users] (no subject)

[Navneet Kumar Singh]

I have seen this in Gromacs manual.

[ virtual_sites2 ]
; Site  fromfunct  a
5   1 2 1  0.7439756

for type 3 like this:

[ virtual_sites3 ]
; Site  from   funct   a  b
5   1 2 3  1   0.7439756  0.128012

for type 3fd like this:

[ virtual_sites3 ]
; Site  from   funct   a  d
5   1 2 3  2   0.5-0.105

for type 3fad like this:

[ virtual_sites3 ]
; Site  from   funct   theta  d
5   1 2 3  3   1200.5

for type 3out like this:

[ virtual_sites3 ]
; Site  from   funct   a  b  c
5   1 2 3  4   -0.4   -0.4   6.9281

for type 4fdn like this:

[ virtual_sites4 ]
; Site  from  funct   a  b  c
5   1 2 3 4   2   1.00.9   0.105

__


I have this from unk.itp file.

[ virtual_sites3 ]
; Site   from funct a   d
   52 12323 2 0   -0.164

[ exclusions ]
; ai  aj
152 1
   5223 1
   5221 1
   5222 1
   5218 1
   5219 1
   5251 1
   5250 1


Now I have to add this in topology file. Is this supposed to add in
system.top ?

On Tue, Aug 27, 2019 at 12:11 AM Justin Lemkul  wrote:

>
>
> On 8/26/19 2:33 PM, Navneet Kumar Singh wrote:
> > I can't understand meaning of this "For all other GROMACS versions, you
> > will have to manually edit the topology to use "3fad" construction and
> > appropriate atom numbers." If I am using version other than the
> > Gromacs2016.x.
> >
> > Can I get example of any topology file where these kind of
> construction've
> > for loan pair done manually in the topology file?
>
> Please see the manual for examples of what the different construction
> types are.
>
> -Justin
>
> > On Mon, Aug 26, 2019 at 11:57 PM Justin Lemkul  wrote:
> >
> >>
> >> On 8/26/19 1:14 PM, Navneet Kumar Singh wrote:
> >>> Do I have to add vsite3 information from unk.itp to system.top files?
> >> That directive belongs in the topology to which it corresponds. If it is
> >> in unk.itp, then it is already in system.top. You don't need to include
> >> anything else.
> >>
> >> -Justin
> >>
> >>> -maxwarn 1 flag I checked in gromacs 16 version and it's running there.
> >>>
> >>> On Mon, 26 Aug 2019, 00:58 Justin Lemkul,  wrote:
> >>>
>  On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:
> > Yeah! I have read that.
> >
> > uses -maxwarn 1 to produce .tpr file using grompp command as
> mentioned
> >> in
>  Since you are getting an error rather than a warning, that means you
> are
>  not using GROMACS 2016.x, as the instructions I pointed to you say.
> 
>  If you want to use a different GROMACS version, you have to change the
>  topology. Again see the link I provided for a description of what to
> do.
> 
>  -Justin
> 
> > python script cgenff_charmm2gmx_py2.py
> >
> > output of cgenff_charmm2gmx_py2.py
> >
> >>
> _
> > NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16
> (default,
>  Mar
> > 26 2019, 10:00:46)
> > [GCC 5.4.0 20160609]
> >
> > NOTE 2: Please be sure to use the same version of CGenFF in your
> > simulations that was used during parameter generation:
> > --Version of CGenFF detected in  unk.str : 4.0
> > --Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc :
> >> 4.0
> > NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
> > parameters that are already in CGenFF' option when uploading a
> molecule
> > into CGenFF.
> >
> > NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.
>  This
> > is not a problem, just FYI!
> >
> >  DONE 
> > Conversion complete.
> > The molecule topology has been written to unk.itp
> > Additional parameters needed by the molecule are written to unk.prm,
>  which
> > needs to be included in the system .top
> >
> > PLEASE NOTE: lone pair construction requires duplicate host atom
> >> numbers,
> > which will make grompp complain
> > To produce .tpr files, the user MUST use -maxwarn 1 to circumvent
> this
>  check
> 
> >>
> 
> > After that I am using same -maxwarn 1 but still, it's giving error.
> It
>  may
> > be some silly 

Re: [gmx-users] (no subject)

[Justin Lemkul]

On 8/26/19 2:33 PM, Navneet Kumar Singh wrote:

I can't understand meaning of this "For all other GROMACS versions, you
will have to manually edit the topology to use "3fad" construction and
appropriate atom numbers." If I am using version other than the
Gromacs2016.x.

Can I get example of any topology file where these kind of construction've
for loan pair done manually in the topology file?


Please see the manual for examples of what the different construction 
types are.


-Justin


On Mon, Aug 26, 2019 at 11:57 PM Justin Lemkul  wrote:



On 8/26/19 1:14 PM, Navneet Kumar Singh wrote:

Do I have to add vsite3 information from unk.itp to system.top files?

That directive belongs in the topology to which it corresponds. If it is
in unk.itp, then it is already in system.top. You don't need to include
anything else.

-Justin


-maxwarn 1 flag I checked in gromacs 16 version and it's running there.

On Mon, 26 Aug 2019, 00:58 Justin Lemkul,  wrote:


On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:

Yeah! I have read that.

uses -maxwarn 1 to produce .tpr file using grompp command as mentioned

in

Since you are getting an error rather than a warning, that means you are
not using GROMACS 2016.x, as the instructions I pointed to you say.

If you want to use a different GROMACS version, you have to change the
topology. Again see the link I provided for a description of what to do.

-Justin


python script cgenff_charmm2gmx_py2.py

output of cgenff_charmm2gmx_py2.py


_

NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default,

Mar

26 2019, 10:00:46)
[GCC 5.4.0 20160609]

NOTE 2: Please be sure to use the same version of CGenFF in your
simulations that was used during parameter generation:
--Version of CGenFF detected in  unk.str : 4.0
--Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc :

4.0

NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
parameters that are already in CGenFF' option when uploading a molecule
into CGenFF.

NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.

This

is not a problem, just FYI!

 DONE 
Conversion complete.
The molecule topology has been written to unk.itp
Additional parameters needed by the molecule are written to unk.prm,

which

needs to be included in the system .top

PLEASE NOTE: lone pair construction requires duplicate host atom

numbers,

which will make grompp complain
To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this

check




After that I am using same -maxwarn 1 but still, it's giving error. It

may

be some silly mistake please let me know.


On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul  wrote:


On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:

Thank You Sir!

Attached file can be downloaded from following link.

https://fil.email/OR7Nsh0f


Error

ERROR 1 [file unk.itp, line 497]:
  Duplicate atom index (23) in virtual_sites3
___

It support lone pair construction for halogens only. Please suggest

some

alternatives.

The link I provided before describes what you need to do. Please

consult

that information.

-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

==

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==

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

==

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send a mail to 

Re: [gmx-users] (no subject)

[Navneet Kumar Singh]

I can't understand meaning of this "For all other GROMACS versions, you
will have to manually edit the topology to use "3fad" construction and
appropriate atom numbers." If I am using version other than the
Gromacs2016.x.

Can I get example of any topology file where these kind of construction've
for loan pair done manually in the topology file?

On Mon, Aug 26, 2019 at 11:57 PM Justin Lemkul  wrote:

>
>
> On 8/26/19 1:14 PM, Navneet Kumar Singh wrote:
> > Do I have to add vsite3 information from unk.itp to system.top files?
>
> That directive belongs in the topology to which it corresponds. If it is
> in unk.itp, then it is already in system.top. You don't need to include
> anything else.
>
> -Justin
>
> > -maxwarn 1 flag I checked in gromacs 16 version and it's running there.
> >
> > On Mon, 26 Aug 2019, 00:58 Justin Lemkul,  wrote:
> >
> >>
> >> On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:
> >>> Yeah! I have read that.
> >>>
> >>> uses -maxwarn 1 to produce .tpr file using grompp command as mentioned
> in
> >> Since you are getting an error rather than a warning, that means you are
> >> not using GROMACS 2016.x, as the instructions I pointed to you say.
> >>
> >> If you want to use a different GROMACS version, you have to change the
> >> topology. Again see the link I provided for a description of what to do.
> >>
> >> -Justin
> >>
> >>> python script cgenff_charmm2gmx_py2.py
> >>>
> >>> output of cgenff_charmm2gmx_py2.py
> >>>
> >>
> _
> >>> NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default,
> >> Mar
> >>> 26 2019, 10:00:46)
> >>> [GCC 5.4.0 20160609]
> >>>
> >>> NOTE 2: Please be sure to use the same version of CGenFF in your
> >>> simulations that was used during parameter generation:
> >>> --Version of CGenFF detected in  unk.str : 4.0
> >>> --Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc :
> 4.0
> >>>
> >>> NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
> >>> parameters that are already in CGenFF' option when uploading a molecule
> >>> into CGenFF.
> >>>
> >>> NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.
> >> This
> >>> is not a problem, just FYI!
> >>>
> >>>  DONE 
> >>> Conversion complete.
> >>> The molecule topology has been written to unk.itp
> >>> Additional parameters needed by the molecule are written to unk.prm,
> >> which
> >>> needs to be included in the system .top
> >>>
> >>> PLEASE NOTE: lone pair construction requires duplicate host atom
> numbers,
> >>> which will make grompp complain
> >>> To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this
> >> check
> >>
> 
> >>> After that I am using same -maxwarn 1 but still, it's giving error. It
> >> may
> >>> be some silly mistake please let me know.
> >>>
> >>>
> >>> On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul  wrote:
> >>>
>  On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:
> > Thank You Sir!
> >
> > Attached file can be downloaded from following link.
> >
> > https://fil.email/OR7Nsh0f
> > 
> > 
> > Error
> >
> > ERROR 1 [file unk.itp, line 497]:
> >  Duplicate atom index (23) in virtual_sites3
> > ___
> >
> > It support lone pair construction for halogens only. Please suggest
> >> some
> > alternatives.
>  The link I provided before describes what you need to do. Please
> consult
>  that information.
> 
>  -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
> 

Re: [gmx-users] (no subject)

[Justin Lemkul]

On 8/26/19 1:14 PM, Navneet Kumar Singh wrote:

Do I have to add vsite3 information from unk.itp to system.top files?


That directive belongs in the topology to which it corresponds. If it is 
in unk.itp, then it is already in system.top. You don't need to include 
anything else.


-Justin


-maxwarn 1 flag I checked in gromacs 16 version and it's running there.

On Mon, 26 Aug 2019, 00:58 Justin Lemkul,  wrote:



On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:

Yeah! I have read that.

uses -maxwarn 1 to produce .tpr file using grompp command as mentioned in

Since you are getting an error rather than a warning, that means you are
not using GROMACS 2016.x, as the instructions I pointed to you say.

If you want to use a different GROMACS version, you have to change the
topology. Again see the link I provided for a description of what to do.

-Justin


python script cgenff_charmm2gmx_py2.py

output of cgenff_charmm2gmx_py2.py


_

NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default,

Mar

26 2019, 10:00:46)
[GCC 5.4.0 20160609]

NOTE 2: Please be sure to use the same version of CGenFF in your
simulations that was used during parameter generation:
--Version of CGenFF detected in  unk.str : 4.0
--Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc : 4.0

NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
parameters that are already in CGenFF' option when uploading a molecule
into CGenFF.

NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.

This

is not a problem, just FYI!

 DONE 
Conversion complete.
The molecule topology has been written to unk.itp
Additional parameters needed by the molecule are written to unk.prm,

which

needs to be included in the system .top

PLEASE NOTE: lone pair construction requires duplicate host atom numbers,
which will make grompp complain
To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this

check


After that I am using same -maxwarn 1 but still, it's giving error. It

may

be some silly mistake please let me know.


On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul  wrote:


On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:

Thank You Sir!

Attached file can be downloaded from following link.

https://fil.email/OR7Nsh0f


Error

ERROR 1 [file unk.itp, line 497]:
 Duplicate atom index (23) in virtual_sites3
___

It support lone pair construction for halogens only. Please suggest

some

alternatives.

The link I provided before describes what you need to do. Please consult
that information.

-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

==

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--
==

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

==

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--
==

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

==

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Re: [gmx-users] (no subject)

[Navneet Kumar Singh]

Do I have to add vsite3 information from unk.itp to system.top files?

-maxwarn 1 flag I checked in gromacs 16 version and it's running there.

On Mon, 26 Aug 2019, 00:58 Justin Lemkul,  wrote:

>
>
> On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:
> > Yeah! I have read that.
> >
> > uses -maxwarn 1 to produce .tpr file using grompp command as mentioned in
>
> Since you are getting an error rather than a warning, that means you are
> not using GROMACS 2016.x, as the instructions I pointed to you say.
>
> If you want to use a different GROMACS version, you have to change the
> topology. Again see the link I provided for a description of what to do.
>
> -Justin
>
> > python script cgenff_charmm2gmx_py2.py
> >
> > output of cgenff_charmm2gmx_py2.py
> >
> _
> >
> > NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default,
> Mar
> > 26 2019, 10:00:46)
> > [GCC 5.4.0 20160609]
> >
> > NOTE 2: Please be sure to use the same version of CGenFF in your
> > simulations that was used during parameter generation:
> > --Version of CGenFF detected in  unk.str : 4.0
> > --Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc : 4.0
> >
> > NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
> > parameters that are already in CGenFF' option when uploading a molecule
> > into CGenFF.
> >
> > NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.
> This
> > is not a problem, just FYI!
> >
> >  DONE 
> > Conversion complete.
> > The molecule topology has been written to unk.itp
> > Additional parameters needed by the molecule are written to unk.prm,
> which
> > needs to be included in the system .top
> >
> > PLEASE NOTE: lone pair construction requires duplicate host atom numbers,
> > which will make grompp complain
> > To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this
> check
> >
> 
> >
> > After that I am using same -maxwarn 1 but still, it's giving error. It
> may
> > be some silly mistake please let me know.
> >
> >
> > On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul  wrote:
> >
> >>
> >> On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:
> >>> Thank You Sir!
> >>>
> >>> Attached file can be downloaded from following link.
> >>>
> >>> https://fil.email/OR7Nsh0f
> >>> 
> >>> 
> >>> Error
> >>>
> >>> ERROR 1 [file unk.itp, line 497]:
> >>> Duplicate atom index (23) in virtual_sites3
> >>> ___
> >>>
> >>> It support lone pair construction for halogens only. Please suggest
> some
> >>> alternatives.
> >> The link I provided before describes what you need to do. Please consult
> >> that information.
> >>
> >> -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.
>
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:

Yeah! I have read that.

uses -maxwarn 1 to produce .tpr file using grompp command as mentioned in


Since you are getting an error rather than a warning, that means you are 
not using GROMACS 2016.x, as the instructions I pointed to you say.


If you want to use a different GROMACS version, you have to change the 
topology. Again see the link I provided for a description of what to do.


-Justin


python script cgenff_charmm2gmx_py2.py

output of cgenff_charmm2gmx_py2.py
_

NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default, Mar
26 2019, 10:00:46)
[GCC 5.4.0 20160609]

NOTE 2: Please be sure to use the same version of CGenFF in your
simulations that was used during parameter generation:
--Version of CGenFF detected in  unk.str : 4.0
--Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc : 4.0

NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
parameters that are already in CGenFF' option when uploading a molecule
into CGenFF.

NOTE 4: 1 lone pairs found in topology that are not in the mol2 file. This
is not a problem, just FYI!

 DONE 
Conversion complete.
The molecule topology has been written to unk.itp
Additional parameters needed by the molecule are written to unk.prm, which
needs to be included in the system .top

PLEASE NOTE: lone pair construction requires duplicate host atom numbers,
which will make grompp complain
To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this check


After that I am using same -maxwarn 1 but still, it's giving error. It may
be some silly mistake please let me know.


On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul  wrote:



On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:

Thank You Sir!

Attached file can be downloaded from following link.

https://fil.email/OR7Nsh0f


Error

ERROR 1 [file unk.itp, line 497]:
Duplicate atom index (23) in virtual_sites3
___

It support lone pair construction for halogens only. Please suggest some
alternatives.

The link I provided before describes what you need to do. Please consult
that information.

-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

==

--
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] (no subject)

[Navneet Kumar Singh]

Yeah! I have read that.

uses -maxwarn 1 to produce .tpr file using grompp command as mentioned in
python script cgenff_charmm2gmx_py2.py

output of cgenff_charmm2gmx_py2.py
_

NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default, Mar
26 2019, 10:00:46)
[GCC 5.4.0 20160609]

NOTE 2: Please be sure to use the same version of CGenFF in your
simulations that was used during parameter generation:
--Version of CGenFF detected in  unk.str : 4.0
--Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc : 4.0

NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
parameters that are already in CGenFF' option when uploading a molecule
into CGenFF.

NOTE 4: 1 lone pairs found in topology that are not in the mol2 file. This
is not a problem, just FYI!

 DONE 
Conversion complete.
The molecule topology has been written to unk.itp
Additional parameters needed by the molecule are written to unk.prm, which
needs to be included in the system .top

PLEASE NOTE: lone pair construction requires duplicate host atom numbers,
which will make grompp complain
To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this check


After that I am using same -maxwarn 1 but still, it's giving error. It may
be some silly mistake please let me know.


On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul  wrote:

>
>
> On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:
> > Thank You Sir!
> >
> > Attached file can be downloaded from following link.
> >
> > https://fil.email/OR7Nsh0f
> > 
> > 
> > Error
> >
> > ERROR 1 [file unk.itp, line 497]:
> >Duplicate atom index (23) in virtual_sites3
> > ___
> >
> > It support lone pair construction for halogens only. Please suggest some
> > alternatives.
>
> The link I provided before describes what you need to do. Please consult
> that information.
>
> -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.
>


-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:

Thank You Sir!

Attached file can be downloaded from following link.

https://fil.email/OR7Nsh0f


Error

ERROR 1 [file unk.itp, line 497]:
   Duplicate atom index (23) in virtual_sites3
___

It support lone pair construction for halogens only. Please suggest some
alternatives.


The link I provided before describes what you need to do. Please consult 
that information.


-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 
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Re: [gmx-users] (no subject)

[Navneet Kumar Singh]

Thank You Sir!

Attached file can be downloaded from following link.

https://fil.email/OR7Nsh0f


Error

ERROR 1 [file unk.itp, line 497]:
  Duplicate atom index (23) in virtual_sites3
___

It support lone pair construction for halogens only. Please suggest some
alternatives.

On Sun, Aug 25, 2019 at 8:11 PM Justin Lemkul  wrote:

>
>
> On 8/25/19 8:33 AM, Navneet Kumar Singh wrote:
> > can you please help in solving this error while running MD simulation of
> > protein-ligand complex using CHARMM36 force field on GROMACS engine.
> >
> >
> >
> > *Command*
> >
> > *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr*
> >
> >
> > *ERROR*
> >
> >
> > *ERROR 1 [file unk.itp, line 497]:  Duplicate atom index (23) in
> > virtual_sites3*
> >
> >
> >
> **
> >
> > *unk.itp file indicated error/ Please find the attached file for more
> > details.*
>
> The mailing list does not accept attachments.
>
> Please see the information at
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs which
> specifically addresses this lone pair issue and how to deal with it.
> GROMACS does not easily support the kinds of lone pair/vsite
> construction that CHARMM requires for this kind of interaction.
>
> -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.
>


-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
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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* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] (no subject)

[Justin Lemkul]

On 8/25/19 8:33 AM, Navneet Kumar Singh wrote:

can you please help in solving this error while running MD simulation of
protein-ligand complex using CHARMM36 force field on GROMACS engine.



*Command*

*gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr*


*ERROR*


*ERROR 1 [file unk.itp, line 497]:  Duplicate atom index (23) in
virtual_sites3*


**

*unk.itp file indicated error/ Please find the attached file for more
details.*


The mailing list does not accept attachments.

Please see the information at 
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs which 
specifically addresses this lone pair issue and how to deal with it. 
GROMACS does not easily support the kinds of lone pair/vsite 
construction that CHARMM requires for this kind of interaction.


-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 
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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mail to gmx-users-requ...@gromacs.org.

[gmx-users] (no subject)

[Navneet Kumar Singh]

can you please help in solving this error while running MD simulation of
protein-ligand complex using CHARMM36 force field on GROMACS engine.



*Command*

*gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr*


*ERROR*


*ERROR 1 [file unk.itp, line 497]:  Duplicate atom index (23) in
virtual_sites3*


**

*unk.itp file indicated error/ Please find the attached file for more
details.*


















*   192223 1 9   19222321 9   512223 1
9   51222321 9[ virtual_sites3 ]; Site   from funct a   d   52
12323 2 0   -0.164[ exclusions ]; ai  aj152 1
 5223 1   5221 1   5222 1   5218 1   5219 1   5251
1   5250 1*


*___*

*CGenFF Server was used to prepare the toplogy and other required files for
th e small molecules*



-- 






-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 8/19/19 2:00 AM, Priyanka Singh wrote:

Hii
I am new to simulations. I want to ask is it ok to use ligand topology
build using PRODRG server if using amber force field for RNA-ligand
simulation. what precautions one should take ends of the RNA molecule.
PRODRG is for GROMOS and produces very low-quality topologies. You 
cannot combine GROMOS topologies with AMBER (nor can you mix and match 
any force fields). Do everything with one force field. AMBER + GAFF is a 
much better option.


-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

==

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Re: [gmx-users] (no subject)

[Jorden Cabal]

I think the answer is not so straightforward. It depends upon a lot of
things, but I would say that the parameters derived using QM is better. If
you do not have any other options you can still use PRODRG server but even
in that case, I find many people using the docked (or bound) conformation
of the Ligand molecule to generate the initial parameters, which in my view
should not be done. One should generate the parameters using the molecule
in its minimum energy conformation instead of bound conformation.
I would also suggest you to look at the RED server. Please follow this link
https://upjv.q4md-forcefieldtools.org/RED/

Thank you

On Mon, Aug 19, 2019 at 3:00 PM Priyanka Singh 
wrote:

> Hii
> I am new to simulations. I want to ask is it ok to use ligand topology
> build using PRODRG server if using amber force field for RNA-ligand
> simulation. what precautions one should take ends of the RNA molecule.
> --
> Gromacs Users mailing list
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[gmx-users] (no subject)

[Priyanka Singh]

Hii
I am new to simulations. I want to ask is it ok to use ligand topology
build using PRODRG server if using amber force field for RNA-ligand
simulation. what precautions one should take ends of the RNA molecule.
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[gmx-users] (no subject)

[Pradeepa Kumari]

pradeepakumar...@gmail.com
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[gmx-users] (no subject)

[Maria Luisa]

Dear user.
I have a problem. I have to simulate a box of 100 molecules of
polyvinylidene fluoride (PVDF) and 1436 molecules of the solvent ATBC. At
first I built the single chain of PVDf and a single molecules of ATBC, and
I was able to construct topology using opls force-field. The command that
I used is gmx x2top. When I create the complete box with a total amount of
95320 atoms, an error occurs saying to me that it's possible recognize
only 1800 atoms of 95320. This is strange, because the two molecules are
written in the topology file each one, but not together in the box. What
is the problem? Is there some bug with my version of gromacs (5.1.4)?

I wait for your answer
Maria Luisa


Maria Luisa Perrotta
Ph.D Student, CNR-ITM
via P.Bucci, 87036 Rende (Cs)
Italy
email: ml.perro...@itm.cnr.it


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[gmx-users] (no subject)

[Negar Parvizi]

Dear all,
I have a protein_Ligand complex which I want  do Umbrella Sampling on it to 
find out free energy.for this purpose I used Justin tutorial(Tutorial 3: 
Umbrella Sampling: GROMACS Tutorial ).

  
|  
|  
 |  
GROMACS Tutorial
  | 
 |

 |

 
Here is my questiones:in tutorial he said:
Acetylated at the N-terminus of each chain of wild-type Aβ protofibril and 
after pdb2gmx command; he said choose:
"None" for the N-termini, and "COO-" for the C-termini1 - why he said  COO-" 
for the C-termini?2- I don't know how should I do for my own Protein_Ligand 
complex? what points should  be paied attention to find out where adding 
acetyl, COO or NH2?

I would  appreciate any help
Tanks in advance,
Negar
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[gmx-users] (no subject)

[Mahsa Rezaei]

mahs.rez...@mail.sbu.ac.ir
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[gmx-users] (no subject)

[Meenakshi Choudhry]

ok
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[gmx-users] (no subject)

[pkalita]

* * * D I S C L A I M E R * * *
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Re: [gmx-users] (no subject) (Soham Sarkar)

[Soham Sarkar]

Hello,
 The "?" You are talking about is mistakenly written there. The
original itp file has nothing there and is showing the error. The first few
lines are commented out. So why is that problem? Sorry for not giving a
title. If you want, I can share the original itp file here but as per the
rule I can not attach any sort of files here. So now please tell me what
could be the problem?

On Fri, 5 Apr 2019, 3:26 pm ABEL Stephane,  wrote:

> Hi
>
> In your itp you have a "?"
>
> ?; GENERATED BY LigParGen Server
>
> Remove it and the problem will be solved
>
> PS : next time add a title in you message.
>
> Good luck
>
> -
> --
>
> Message: 1
> Date: Fri, 5 Apr 2019 14:26:00 +0530
> From: Soham Sarkar 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] (no subject)
> Message-ID:
> <
> ca+fbedfs1gay1d5k-zvdv9fgmzxfenf-ia-mwetruuqbwpm...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear all,
> I am using GROMACS-2018. I want to simulate a system which contain
> Tertiary Butyl alcohol (TBA) in it. I am facing problems while executing
> the GROMPP command. I have defined this residue in aminoacids.rtp.
>
> The error is like
>
> "NOTE 1 [file ions.mdp]:
>   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>   that with the Verlet scheme, nstlist has no effect on the accuracy of
>   your simulation.
>
> Setting the LD random seed to 918407885
>
> WARNING 1 [file tba.itp, line 1]:
>   Too few gb parameters for type ?
>
>
> Couldn't find topology match for atomtype ?
> Aborted (core dumped)"
>  I have generated the itp file for TBA from ligpargen.
>
> My itp file is
>
> ;
> ?; GENERATED BY LigParGen Server
> ; Jorgensen Lab @ Yale University
> ;
>
> [ atomtypes ]
>   opls_135C112.0110 0.000A3.5E-01   2.76144E-01
>   opls_140   H11 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_140   H12 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_140   H13 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_159C212.0110 0.000A3.5E-01   2.76144E-01
>   opls_135C312.0110 0.000A3.5E-01   2.76144E-01
>   opls_140   H31 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_140   H32 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_140   H33 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_154O415.9990 0.000A3.12000E-01   7.11280E-01
>   opls_155   H41 1.0080 0.000A0.0E+00   0.0E+00
>   opls_135C512.0110 0.000A3.5E-01   2.76144E-01
>   opls_140   H51 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_140   H52 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_140   H53 1.0080 0.000A2.5E-01   1.25520E-01
>
> [ moleculetype ]
> ; Name   nrexcl
> TBA   3
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr charge   mass
>  1   opls_135  1TBAC1  1-0.304408  12.0110
>  2   opls_140  1TBA   H11  1 0.098297   1.0080
>  3   opls_140  1TBA   H12  1 0.086235   1.0080
>  4   opls_140  1TBA   H13  1 0.111410   1.0080
>  5   opls_159  1TBAC2  1 0.247098  12.0110
>  6   opls_135  1TBAC3  1-0.299728  12.0110
>  7   opls_140  1TBA   H31  1 0.101177   1.0080
>  8   opls_140  1TBA   H32  1 0.110693   1.0080
>  9   opls_140  1TBA   H33  1 0.110695   1.0080
> 10   opls_154  1TBAO4  1-0.550587  15.9990
> 11   opls_155  1TBA   H41  1 0.297574   1.0080
> 12   opls_135  1TBAC5  1-0.304401  12.0110
> 13   opls_140  1TBA   H51  1 0.098298   1.0080
> 14   opls_140  1TBA   H52  1 0.086234   1.0080
> 15   opls_140  1TBA   H53  1 0.111413   1.0080
> [ bonds ]
> 2 1 1  0.1090 284512.000
> 3 1 1  0.1090 284512.000
> 4 1 1  0.1090 284512.000
> 5 1 1  0.1529 224262.400
> 6 5 1  0.1529 224262.400
> 7 6 1  0.1090 284512.000
> 8 6 1  0.1090 284512.000
> 9 6 1  0.1090 284512.000
>10 5 1  0.1410 267776.000
>1110 1  0.0945 462750.400
>12 5 1  0.1529 224262.400
>1312 1  0.109

[gmx-users] (no subject) (Soham Sarkar)

[ABEL Stephane]

Hi 

In your itp you have a "?" 

?; GENERATED BY LigParGen Server

Remove it and the problem will be solved 

PS : next time add a title in you message. 

Good luck 

-
--

Message: 1
Date: Fri, 5 Apr 2019 14:26:00 +0530
From: Soham Sarkar 
To: gmx-us...@gromacs.org
Subject: [gmx-users] (no subject)
Message-ID:

Content-Type: text/plain; charset="UTF-8"

Dear all,
I am using GROMACS-2018. I want to simulate a system which contain
Tertiary Butyl alcohol (TBA) in it. I am facing problems while executing
the GROMPP command. I have defined this residue in aminoacids.rtp.

The error is like

"NOTE 1 [file ions.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 918407885

WARNING 1 [file tba.itp, line 1]:
  Too few gb parameters for type ?


Couldn't find topology match for atomtype ?
Aborted (core dumped)"
 I have generated the itp file for TBA from ligpargen.

My itp file is

;
?; GENERATED BY LigParGen Server
; Jorgensen Lab @ Yale University
;

[ atomtypes ]
  opls_135C112.0110 0.000A3.5E-01   2.76144E-01
  opls_140   H11 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H12 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H13 1.0080 0.000A2.5E-01   1.25520E-01
  opls_159C212.0110 0.000A3.5E-01   2.76144E-01
  opls_135C312.0110 0.000A3.5E-01   2.76144E-01
  opls_140   H31 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H32 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H33 1.0080 0.000A2.5E-01   1.25520E-01
  opls_154O415.9990 0.000A3.12000E-01   7.11280E-01
  opls_155   H41 1.0080 0.000A0.0E+00   0.0E+00
  opls_135C512.0110 0.000A3.5E-01   2.76144E-01
  opls_140   H51 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H52 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H53 1.0080 0.000A2.5E-01   1.25520E-01

[ moleculetype ]
; Name   nrexcl
TBA   3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
 1   opls_135  1TBAC1  1-0.304408  12.0110
 2   opls_140  1TBA   H11  1 0.098297   1.0080
 3   opls_140  1TBA   H12  1 0.086235   1.0080
 4   opls_140  1TBA   H13  1 0.111410   1.0080
 5   opls_159  1TBAC2  1 0.247098  12.0110
 6   opls_135  1TBAC3  1-0.299728  12.0110
 7   opls_140  1TBA   H31  1 0.101177   1.0080
 8   opls_140  1TBA   H32  1 0.110693   1.0080
 9   opls_140  1TBA   H33  1 0.110695   1.0080
10   opls_154  1TBAO4  1-0.550587  15.9990
11   opls_155  1TBA   H41  1 0.297574   1.0080
12   opls_135  1TBAC5  1-0.304401  12.0110
13   opls_140  1TBA   H51  1 0.098298   1.0080
14   opls_140  1TBA   H52  1 0.086234   1.0080
15   opls_140  1TBA   H53  1 0.111413   1.0080
[ bonds ]
2 1 1  0.1090 284512.000
3 1 1  0.1090 284512.000
4 1 1  0.1090 284512.000
5 1 1  0.1529 224262.400
6 5 1  0.1529 224262.400
7 6 1  0.1090 284512.000
8 6 1  0.1090 284512.000
9 6 1  0.1090 284512.000
   10 5 1  0.1410 267776.000
   1110 1  0.0945 462750.400
   12 5 1  0.1529 224262.400
   1312 1  0.1090 284512.000
   1412 1  0.1090 284512.000
   1512 1  0.1090 284512.000

[ angles ]
;  aiajak functc0c1
c2c3
2 1 3 1107.800276.144
2 1 4 1107.800276.144
2 1 5 1110.700313.800
1 5 6 1112.700488.273
5 6 7 1110.700313.800
5 6 8 1110.700313.800
5 6 9 1110.700313.800
1 510 1109.500418.400
51011 1108.500460.240
1 512 1112.700488.273
51213 1110.700313.800
51214 1110.700313.800
51215 1110.700313.800
7 6 9 1107.800276.144
6 510 1109.500418.400
3 1 4 1107.800276.144
4 1 5 1110.700313.800
3 1 5 1110.700313.800
   10 512 1109.50

[gmx-users] (no subject)

[Soham Sarkar]

Dear all,
I am using GROMACS-2018. I want to simulate a system which contain
Tertiary Butyl alcohol (TBA) in it. I am facing problems while executing
the GROMPP command. I have defined this residue in aminoacids.rtp.

The error is like

"NOTE 1 [file ions.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 918407885

WARNING 1 [file tba.itp, line 1]:
  Too few gb parameters for type 


Couldn't find topology match for atomtype 
Aborted (core dumped)"
 I have generated the itp file for TBA from ligpargen.

My itp file is

;
; GENERATED BY LigParGen Server
; Jorgensen Lab @ Yale University
;

[ atomtypes ]
  opls_135C112.0110 0.000A3.5E-01   2.76144E-01
  opls_140   H11 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H12 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H13 1.0080 0.000A2.5E-01   1.25520E-01
  opls_159C212.0110 0.000A3.5E-01   2.76144E-01
  opls_135C312.0110 0.000A3.5E-01   2.76144E-01
  opls_140   H31 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H32 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H33 1.0080 0.000A2.5E-01   1.25520E-01
  opls_154O415.9990 0.000A3.12000E-01   7.11280E-01
  opls_155   H41 1.0080 0.000A0.0E+00   0.0E+00
  opls_135C512.0110 0.000A3.5E-01   2.76144E-01
  opls_140   H51 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H52 1.0080 0.000A2.5E-01   1.25520E-01
  opls_140   H53 1.0080 0.000A2.5E-01   1.25520E-01

[ moleculetype ]
; Name   nrexcl
TBA   3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
 1   opls_135  1TBAC1  1-0.304408  12.0110
 2   opls_140  1TBA   H11  1 0.098297   1.0080
 3   opls_140  1TBA   H12  1 0.086235   1.0080
 4   opls_140  1TBA   H13  1 0.111410   1.0080
 5   opls_159  1TBAC2  1 0.247098  12.0110
 6   opls_135  1TBAC3  1-0.299728  12.0110
 7   opls_140  1TBA   H31  1 0.101177   1.0080
 8   opls_140  1TBA   H32  1 0.110693   1.0080
 9   opls_140  1TBA   H33  1 0.110695   1.0080
10   opls_154  1TBAO4  1-0.550587  15.9990
11   opls_155  1TBA   H41  1 0.297574   1.0080
12   opls_135  1TBAC5  1-0.304401  12.0110
13   opls_140  1TBA   H51  1 0.098298   1.0080
14   opls_140  1TBA   H52  1 0.086234   1.0080
15   opls_140  1TBA   H53  1 0.111413   1.0080
[ bonds ]
2 1 1  0.1090 284512.000
3 1 1  0.1090 284512.000
4 1 1  0.1090 284512.000
5 1 1  0.1529 224262.400
6 5 1  0.1529 224262.400
7 6 1  0.1090 284512.000
8 6 1  0.1090 284512.000
9 6 1  0.1090 284512.000
   10 5 1  0.1410 267776.000
   1110 1  0.0945 462750.400
   12 5 1  0.1529 224262.400
   1312 1  0.1090 284512.000
   1412 1  0.1090 284512.000
   1512 1  0.1090 284512.000

[ angles ]
;  aiajak functc0c1
c2c3
2 1 3 1107.800276.144
2 1 4 1107.800276.144
2 1 5 1110.700313.800
1 5 6 1112.700488.273
5 6 7 1110.700313.800
5 6 8 1110.700313.800
5 6 9 1110.700313.800
1 510 1109.500418.400
51011 1108.500460.240
1 512 1112.700488.273
51213 1110.700313.800
51214 1110.700313.800
51215 1110.700313.800
7 6 9 1107.800276.144
6 510 1109.500418.400
3 1 4 1107.800276.144
4 1 5 1110.700313.800
3 1 5 1110.700313.800
   10 512 1109.500418.400
   141215 1107.800276.144
   131214 1107.800276.144
7 6 8 1107.800276.144
6 512 1112.700488.273
   131215 1107.800276.144
8 6 9 1107.800276.144

[ dihedrals ]
; IMPROPER DIHEDRAL ANGLES
;  aiajakal functc0c1
c2c3c4c5

[ dihedrals ]
; PROPER DIHEDRAL 

Re: [gmx-users] (no subject)

[Dallas Warren]

In molecular dynamics things move around.

The fact that the molecules aren't in the starting position shows that it
isn't a stable configuration, the interactions between the protein and the
molecules are insufficient to keep them together in that spot.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Thu, 28 Mar 2019 at 05:50, saranya  wrote:

> Hi users,
>
>   I have simulated a protein with gas molecules (CO2,NO2 and SO2) for
> 100ns. I have followed the  protein ligand tutorial. I have applied
> position constraints. After equilibrium the gas molecules are at the docked
> position but at the 60ns simulation the gas molecules are far away from the
> protein. I have applied pBC and sure this is not an visualisatuin error.
> How can I rectify this, Kindly give your valuable suggestions in this
> regard.
>
>
>
> --
>
> *Saranya Vasudevan,*
>
> *Research Scholar,*
>
> *Molecular Quantum Mechanics Laboratory,*
>
> *Department of Physics,*
>
> *Bharathiar University,*
>
> *Coimbatore-46*
> --
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[gmx-users] (no subject)

[saranya]

Hi users,

  I have simulated a protein with gas molecules (CO2,NO2 and SO2) for
100ns. I have followed the  protein ligand tutorial. I have applied
position constraints. After equilibrium the gas molecules are at the docked
position but at the 60ns simulation the gas molecules are far away from the
protein. I have applied pBC and sure this is not an visualisatuin error.
How can I rectify this, Kindly give your valuable suggestions in this
regard.



-- 

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*
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[gmx-users] (no subject)

[shakira shukoor]

Dear all
I encountered with following error when running the umbrella sampling
simulation of a protein. What modification should I make in the pull code
to get rid of the error.

ERROR 1 [file npt_umbrella.mdp]:
  When the maximum distance from a pull group reference atom to other atoms
  in the group is larger than 0.5 times half the box size a centrally
  placed atom should be chosen as pbcatom. Pull group 1 is larger than that
  and does not have a specific atom selected as reference atom.

Pull group  natoms  pbc atom  distance at start  reference at t=0
   1   226   113
   2   226   339   1.396 nm  1.396 nm
Estimate for the relative computational load of the PME mesh part: 0.14
This run will generate roughly 13 Mb of data

Thanks in advance

-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106
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[gmx-users] (no subject)

[Никита Шалин]

Dear Gromacs users,

I would like to buy a videocard for calculation on GPU. I choose between RTX 
2080Ti and Titan Xp. Please, tell me which videocard to choose?


-- 
Искренне Ваш, Никита Шалин
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Re: [gmx-users] (no subject)

[Dallas Warren]

http://manual.gromacs.org/documentation/current/reference-manual/topologies/force-field-organization.html

FFs are located in the share/gromacs/top directory.  If you have your own
FF that isn't included in the distribution with GROMACS, you can either add
it to that directory, or have the FF directory within the directory you run
the simulation.  Then you simply refer the links in your topology files to
that location.

Or are you asking how you can solvate your molecule within ethanol, so you
have it located in an ethanol solution, then run the simulation?  See
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Sat, 9 Feb 2019 at 05:30, Satya Ranjan Sahoo 
wrote:

> Sir,
> Can anyone suggest how I can use ethanol force field to solvate and run MD
> for my molecule. Please help.
>
> On Thu 31 Jan, 2019, 10:48 AM Satya Ranjan Sahoo  wrote:
>
> > Sir,
> > I am a beginner to GROMACS. I was unable to understand how to create all
> > the ions.mdp , md.mdp , mout.mdp , minim.mdp , newbox.mdp , npt.mdp ,
> > nvt.mdp , porse.itp , topol.top input files for molecular simulation of
> my
> > molecule. Please teach me how can I generate or create all the above
> > mentioned input files for my molecule.
> >
> --
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Re: [gmx-users] (no subject)

[Satya Ranjan Sahoo]

Sir,
Can anyone suggest how I can use ethanol force field to solvate and run MD
for my molecule. Please help.

On Thu 31 Jan, 2019, 10:48 AM Satya Ranjan Sahoo  Sir,
> I am a beginner to GROMACS. I was unable to understand how to create all
> the ions.mdp , md.mdp , mout.mdp , minim.mdp , newbox.mdp , npt.mdp ,
> nvt.mdp , porse.itp , topol.top input files for molecular simulation of my
> molecule. Please teach me how can I generate or create all the above
> mentioned input files for my molecule.
>
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Re: [gmx-users] (no subject)

[pbuscemi]

Run the tutorials

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 On Behalf Of Satya
Ranjan Sahoo
Sent: Wednesday, January 30, 2019 11:19 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] (no subject)

Sir,
I am a beginner to GROMACS. I was unable to understand how to create all the
ions.mdp , md.mdp , mout.mdp , minim.mdp , newbox.mdp , npt.mdp , nvt.mdp ,
porse.itp , topol.top input files for molecular simulation of my molecule.
Please teach me how can I generate or create all the above mentioned input
files for my molecule.
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Re: [gmx-users] (no subject)

[Saumyak Mukherjee]

Hi,

There is a detailed online tutorial.
http://www.mdtutorials.com/gmx/

It has everything you need.

Best,
Saumyak

On Thu, 31 Jan 2019 at 10:51, Satya Ranjan Sahoo 
wrote:

> Sir,
> I am a beginner to GROMACS. I was unable to understand how to create all
> the ions.mdp , md.mdp , mout.mdp , minim.mdp , newbox.mdp , npt.mdp ,
> nvt.mdp , porse.itp , topol.top input files for molecular simulation of my
> molecule. Please teach me how can I generate or create all the above
> mentioned input files for my molecule.
> --
> 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.
>


-- 
===
*Saumyak Mukherjee*
Senior Research Fellow
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bengaluru - 560012
===
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[gmx-users] (no subject)

[Satya Ranjan Sahoo]

Sir,
I am a beginner to GROMACS. I was unable to understand how to create all
the ions.mdp , md.mdp , mout.mdp , minim.mdp , newbox.mdp , npt.mdp ,
nvt.mdp , porse.itp , topol.top input files for molecular simulation of my
molecule. Please teach me how can I generate or create all the above
mentioned input files for my molecule.
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Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

This is one of the examples in the documentation of gmx select. Try looking
there!

Mark

On Fri., 25 Jan. 2019, 07:30 Soham Sarkar,  wrote:

> Hello Everyone,
>I want to calculate some properties of the solvent molecules within
> 6angstrom from the protein backbone, for that I need a index group which
> only contain that number of solvent molecules in the index.ndx file so that
> I can specifically select that index to calculate different parameters.
> Please any one help me how would I do that?
> --
> Gromacs Users mailing list
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> * Please search the archive at
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>
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>
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>
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[gmx-users] (no subject)

[Soham Sarkar]

Hello Everyone,
   I want to calculate some properties of the solvent molecules within
6angstrom from the protein backbone, for that I need a index group which
only contain that number of solvent molecules in the index.ndx file so that
I can specifically select that index to calculate different parameters.
Please any one help me how would I do that?
Soham
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[gmx-users] (no subject)

[Soham Sarkar]

Hello Everyone,
   I want to calculate some properties of the solvent molecules within
6angstrom from the protein backbone, for that I need a index group which
only contain that number of solvent molecules in the index.ndx file so that
I can specifically select that index to calculate different parameters.
Please any one help me how would I do that?
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[gmx-users] (no subject)

[marzieh gharouni]

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[gmx-users] (no subject)

[Ahmedmmed Mohammed]

Hello GMX users,
I have old simulation trajectories (.xtc) with their topologies (.tpr). Is
there any way to get energy files (.edr) without rerun the simulations?
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[gmx-users] (no subject)

[maya nair]

ERROR 1 [file res.itp, line 57]:
  Invalid Atomnr j: 4, b2->nr: 3

I am getting the above error for the command

gmx grompp -f em.mdp -c solv.gro -p topol1.top -o ions.tpr. My res.itp file
is given below. I couldnot understand the meaning of this error.  Can you
please help me? part of the .itp is appended here.


   1.

   trial_GMX.top created by acpype (Rev: 0) on Wed Nov 21 15:15:35 2018
   2.
   3.
   4.

   ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
   5.

   1 2 yes 0.5 0.8333
   6.
   7.

   # include "ffnonbonded.itp"
   8.

   # include "ffbonded.itp"
   9.

   # include "gbsa.itp"
   10.
   11.
   12.

   ;name bond_type mass charge ptype sigma epsilon Amb
   13.

   CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
   14.

   oh oh 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104
   15.

   ho ho 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0.
   16.

   ha ha 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150
   17.

   ce ce 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
   18.

   cf cf 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
   19.
   20.
   21.

   ;name nrexcl
   22.

   STL 3
   23.
   24.

   ; nr type resi res atom cgnr charge mass ; qtot bond_type
   25.

   1 CA 1 STL C1 1 0.156600 12.01000 ; qtot 0.157
   26.

   2 oh 1 STL O1 2 -0.494100 16.0 ; qtot -0.338
   27.

   3 ho 1 STL H1 3 0.42 1.00800 ; qtot 0.083
   28.

   4 CA 1 STL C2 4 -0.185000 12.01000 ; qtot -0.103
   29.

   5 ha 1 STL H2 5 0.168000 1.00800 ; qtot 0.066
   30.

   6 oh 1 STL O2 6 -0.494100 16.0 ; qtot -0.429
   31.

   7 ho 1 STL H5 7 0.420500 1.00800 ; qtot -0.008
   32.

   8 CA 1 STL C3 8 0.156600 12.01000 ; qtot 0.149
   33.

   9 oh 1 STL O3 9 -0.494100 16.0 ; qtot -0.346
   34.

   10 ho 1 STL H3 10 0.420500 1.00800 ; qtot 0.075
   35.

   11 CA 1 STL C4 11 -0.24 12.01000 ; qtot -0.165
   36.

   12 ha 1 STL H4 12 0.137000 1.00800 ; qtot -0.028
   37.

   13 CA 1 STL C5 13 0.023200 12.01000 ; qtot -0.005
   38.

   14 CA 1 STL C6 14 -0.24 12.01000 ; qtot -0.245
   39.

   15 ha 1 STL H6 15 0.137000 1.00800 ; qtot -0.108
   40.

   16 ce 1 STL C7 16 -0.121200 12.01000 ; qtot -0.229
   41.

   17 ha 1 STL H7 17 0.13 1.00800 ; qtot -0.099
   42.

   18 cf 1 STL C8 18 -0.085200 12.01000 ; qtot -0.184
   43.

   19 ha 1 STL H8 19 0.126000 1.00800 ; qtot -0.058
   44.

   20 CA 1 STL C9 20 -0.098800 12.01000 ; qtot -0.157
   45.

   21 CA 1 STL C10 21 -0.079500 12.01000 ; qtot -0.237
   46.

   22 ha 1 STL H10 22 0.136000 1.00800 ; qtot -0.101
   47.

   23 CA 1 STL C11 23 -0.187000 12.01000 ; qtot -0.288
   48.

   24 ha 1 STL H11 24 0.143500 1.00800 ; qtot -0.144
   49.

   25 CA 1 STL C12 25 0.131100 12.01000 ; qtot -0.013
   50.

   26 CA 1 STL C13 26 -0.187000 12.01000 ; qtot -0.200
   51.

   27 ha 1 STL H13 27 0.143500 1.00800 ; qtot -0.057
   52.

   28 CA 1 STL C14 28 -0.079500 12.01000 ; qtot -0.136
   53.

   29 ha 1 STL H14 29 0.136000 1.00800 ; qtot 0.000
   54.
   55.
   56.

   ; ai aj funct r k
   57.

   1 4 1 1.3984e-01 3.8585e+05 ; C1 - C2
   58.

   1 9 1 1.3637e-01 3.2133e+05 ; C1 - O3
   59.

   1 14 1 1.3984e-01 3.8585e+05 ; C1 - C6
   60.

   2 3 1 9.7300e-02 3.1079e+05 ; O1 - H1
   61.

   2 25 1 1.3637e-01 3.2133e+05 ; O1 - C12
   62.

   4 5 1 1.0860e-01 2.8937e+05 ; C2 - H2
   63.

   4 8 1 1.3984e-01 3.8585e+05 ; C2 - C3
   64.

   6 7 1 9.7300e-02 3.1079e+05 ; O2 - H5
   65.

   6 8 1 1.3637e-01 3.2133e+05 ; O2 - C3
   66.

   8 11 1 1.3984e-01 3.8585e+05 ; C3 - C4
   67.

   9 10 1 9.7300e-02 3.1079e+05 ; O3 - H3
   68.

   11 12 1 1.0860e-01 2.8937e+05 ; C4 - H4
   69.

   11 13 1 1.3984e-01 3.8585e+05 ; C4 - C5
   70.

   13 14 1 1.3984e-01 3.8585e+05 ; C5 - C6
   71.

   13 16 1 1.4763e-01 3.0234e+05 ; C5 - C7
   72.

   14 15 1 1.0860e-01 2.8937e+05 ; C6 - H6
   73.

   16 17 1 1.0883e-01 2.8660e+05 ; C7 - H7
   74.

   16 18 1 1.3509e-01 4.5070e+05 ; C7 - C8
   75.

   18 19 1 1.0883e-01 2.8660e+05 ; C8 - H8
   76.

   18 20 1 1.4763e-01 3.0234e+05 ; C8 - C9
   77.

   20 21 1 1.3984e-01 3.8585e+05 ; C9 - C10
   78.

   20 28 1 1.3984e-01 3.8585e+05 ; C9 - C14
   79.

   21 22 1 1.0860e-01 2.8937e+05 ; C10 - H10
   80.

   21 23 1 1.3984e-01 3.8585e+05 ; C10 - C11
   81.

   23 24 1 1.0860e-01 2.8937e+05 ; C11 - H11
   82.

   23 25 1 1.3984e-01 3.8585e+05 ; C11 - C12
   83.

   25 26 1 1.3984e-01 3.8585e+05 ; C12 - C13
   84.

   26 27 1 1.0860e-01 2.8937e+05 ; C13 - H13
   85.

   26 28 1 1.3984e-01 3.8585e+05 ; C13 - C14
   86.

   28 29 1 1.0860e-01 2.8937e+05 ; C14 - H14



-- 
Maya S Nair
Assistant Professor
Department of Biotechnology
IIT Roorkee
India
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 12/1/18 8:11 AM, Soham Sarkar wrote:

Dear all,
This is the error I get while executing the grompp command
  " Program grompp, VERSION 4.5.6
Source code file: topio.c, line: 582
Fatal error:
Syntax error - File tris.itp, line 19
Last line read:
' #error CORRECT VERSION OF FORCE FIELD [TPPREV_jun16] WAS NOT "
I gave the command like:
" grompp -f ions.mdp -c solv.gro -o ions.tpr -p system.top
 "
I am attaching the input files. I have generated the tris.itp from tppmktop


Attachments are not allowed on the mailing list.

There are several things to consider. The first is that version 4.5.6 is 
ancient and no longer supported. Use a modern GROMACS version. The 
second is to look at what is in the topology on line 19 to see how not 
to trigger the error that you're getting.


-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

==

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[gmx-users] (no subject)

[Soham Sarkar]

Dear all,
This is the error I get while executing the grompp command
 " Program grompp, VERSION 4.5.6
Source code file: topio.c, line: 582
Fatal error:
Syntax error - File tris.itp, line 19
Last line read:
' #error CORRECT VERSION OF FORCE FIELD [TPPREV_jun16] WAS NOT "
I gave the command like:
" grompp -f ions.mdp -c solv.gro -o ions.tpr -p system.top
 "
I am attaching the input files. I have generated the tris.itp from tppmktop
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 11/23/18 12:58 AM, maya nair wrote:

I am trying to do the molecular dynamics of  DNA-ligand complex. I made the
ligand files using antechamber and converted the amber files to .gro and
.top using acpype.pl. Then I made the complex.gro. when I am trying to run
grommp  ions.mdp and em.mdp, it gives error saying the following

Command line:
   gmx grompp -f ions.mdp -c solv.gro -p topol1.top -o ions.tpr


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
Setting the LD random seed to 2988957772

WARNING 1 [file res.itp, line 5]:
   Too few gb parameters for type 1


Couldn't find topology match for atomtype 1
Aborted (core dumped)

I couldnot understand about the atomtype. I checked in the .atp file and
found that nomenclatures exist there. So couldnot do any rectification.


The .atp file is only read by pdb2gmx, so it's not relevant. Apparently 
you have an atom type "1" (number one) in your topology, which is very 
strange. It doesn't have parameters defined in gb.itp, so you get a 
failure. Make sure your input is sound and your topology/force field 
files are free of typos.



Help me in this regard. I am attaching my files.


This mailing list does not accept attachments. If you need to share 
files, use a file-sharing service and provide the URL.


-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

==

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[gmx-users] (no subject)

[maya nair]

I am trying to do the molecular dynamics of  DNA-ligand complex. I made the
ligand files using antechamber and converted the amber files to .gro and
.top using acpype.pl. Then I made the complex.gro. when I am trying to run
grommp  ions.mdp and em.mdp, it gives error saying the following

Command line:
  gmx grompp -f ions.mdp -c solv.gro -p topol1.top -o ions.tpr


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
Setting the LD random seed to 2988957772

WARNING 1 [file res.itp, line 5]:
  Too few gb parameters for type 1


Couldn't find topology match for atomtype 1
Aborted (core dumped)

I couldnot understand about the atomtype. I checked in the .atp file and
found that nomenclatures exist there. So couldnot do any rectification.
Help me in this regard. I am attaching my files.
Thank you
Maya

[image: Attachments]





-- 
Maya S Nair
Assistant Professor
Department of Biotechnology
IIT Roorkee
India
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[gmx-users] (no subject)

[Ehsan Moravveji]

Dear GMX users,

I would like to share a difficulty installing GROMACS/2018.3 with you. I
use GCC/6.4.0 on a Linux cluster with CentOS 7.5 kernel and GPU nodes
equipped with 4 x P100 Nvidia devices.

Below is the cmake configuration that I use, followed by the error that I
receive. I am not sure if there is still an extra flag to set to resolve
this issue, or some other steps must be taken?

I appreciate your input.

-- 
Kind regards,
Ehsan Moravveji

###
cmake "${cwd}/${dir_src}" \
  -DGMX_SIMD='AVX_512' \
  -DBLAS_mkl_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \
  -DLAPACK_mkl_lapack_LIBRARY="DIR_MKL_LIB/libmkl_sequential.so" \
  -DBLAS_guide_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \
  -DCMAKE_C_COMPILER="${GMX_MPICC}" -DCMAKE_CXX_COMPILER="${GMX_MPICXX}" \
  -DMPI_C_COMPILER="${GMX_MPICC}" -DMPI_CXX_COMPILER="${GMX_MPICXX}" \
  -DCMAKE_MPI_C_COMPILER="${GMX_MPICC}"
-DCMAKE_MPI_CXX_COMPILER="${GMX_MPICXX}" \
  -DCMAKE_INSTALL_PREFIX="${dir_install}" \
  -DCMAKE_PREFIX_PATH="${DIR_MKL_LIB}" \
  -DCMAKE_VERBOSE_MAKEFILE=ON \
  -DGMX_MPI=ON \
  -DGMX_GPU=ON \
  -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF -DEXTRA_CXX_FLAGS="-std=c++11" \
  -DGMX_USE_NVML=ON -DGMX_BUILD_OWN_FFTW=ON \
  -DHWLOC_INCLUDE_DIRS="${EBROOTHWLOC}/include"
-DHWLOC_LIBRARIES="${EBROOTHWLOC}/lib/libhwloc.so" \
  -DCUDA_HOST_COMPILER="${PATH_NVCC}"
-DNVML_INCLUDE_DIR="${EBROOTCUDA}/include" \
  -DNVML_LIBRARY="${EBROOTCUDA}/lib64/stubs/libnvidia-ml.so" \
  -DCUDA_TOOLKIT_ROOT_DIR="${EBROOTCUDA}"
-DCUDA_SDK_ROOT_DIR="${EBROOTCUDA}" \
  -DCUDA_PROPAGATE_HOST_FLAGS=ON -DCUDA_VERBOSE_BUILD=ON \
  -DGMX_CUDA_TARGET_SM="${SM_VER}" -DGMX_CUDA_TARGET_COMPUTE="${SM_VER}" \
  -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF \
  -DCUDA_CUDART_LIBRARY="${EBROOTCUDA}/lib64/libcudart.so"
-DCUDA_CUDA_LIBRARY="${EBROOTCUDA}/lib64/libcuda.so" \

-DCUDA_NVCC_FLAGS="-gencode;arch=compute_${SM_VER},code=compute_${SM_VER};-use_fast_math;-D_FORCE_INLINES"
\
  -DGMX_PREFER_STATIC_LIBS=OFF -DGMX_X11=OFF

###

-- Generating dependency file:
/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.NVCC-depend
/apps/leuven/skylake/2018a/software/CUDA/9.2.148/bin/nvcc -M -D__CUDACC__
/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3/src/gromacs/mdlib/nbnxn_cuda/
nbnxn_cuda.cu -o
/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.NVCC-depend
-ccbin /apps/leuven/skylake/2018a/software/CUDA/9.2.148/bin/nvcc -m64 --std
c++11 -Dlibgromacs_EXPORTS -DGMX_DOUBLE=0 -DHAVE_CONFIG_H
-DUSE_STD_INTTYPES_H -Xcompiler
,\"-mavx512f\",\"-mfma\",\"-fPIC\",\"-O3\",\"-DNDEBUG\",\"-funroll-all-loops\",\"-fexcess-precision=fast\"
-gencode arch=compute_60,code=sm_60 -gencode
arch=compute_60,code=compute_60 -use_fast_math -gencode
arch=compute_60,code=compute_60 -use_fast_math -D_FORCE_INLINES -DNVCC
-I/apps/leuven/skylake/2018a/software/CUDA/9.2.148/include
-I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3/src/external/lmfit
-I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/src/contrib/fftw/fftwBuild-prefix/include
-I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/src
-I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3/src/external/thread_mpi/include
-I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3/src
-I/apps/leuven/skylake/2018a/software/hwloc/1.11.11-GCCcore-6.4.0/include
-I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3/src/external/tng_io/include
-I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/tng/include
nvcc fatal   : 'avx512f': expected a number
CMake Error at libgromacs_generated_nbnxn_cuda.cu.o.Release.cmake:219
(message):
  Error generating

/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda.cu.o
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[gmx-users] (no subject)

[Rakesh Mishra]

Dear Justin its your  conversation  regarding pulling of dsDNA.
Because gromacs is replying as there message is too big so cant be send
and due to that I can not replied in orginal conversation.
But I want to start from the last conversation.

from your side

"It seems to me you have two steps to perform:

1. Extend the duplex to a "ladder-like" conformation
2. Slide one strand past the other

In step 1, I would set the reaction coordinate to be the vector connecting
the terminal *base pairs* (not just one base in one DNA chain) and pull
along that vector in all dimensions. The force will primarily act in one
Cartesian dimension, but by doing it this way, you never have to assume (or
hope) that your system stays nicely aligned along one axis. The pulling
will take some time, and rotation to some extent is inevitable.

In step 2, once the duplex is fully extended, you should be able to do what
you were proposing before, using the terminal single base of each DNA
strand. Again, I still think it's problematic to assume a biasing force in
only one dimension, but that's for you to test.

I'm sorry that I don't have time to look at all the files you sent off-list
or read all the papers you linked. But this is what I can offer as a
suggestion. It's a very difficult system to deal with.

-Justin "


Now my query .

Thanks  for  your lot discussion and advise. So can you tell me please, for
Step First
{In step 1, I would set the reaction coordinate to be the vector connecting
the terminal *base pairs* (not just one base in one DNA chain) and pull
along that vector in all dimensions. The force will primarily act in one
Cartesian dimension, but by doing it this way, you never have to assume (or
hope) that your system stays nicely aligned along one axis. The pulling
will take some time, and rotation to some extent is inevitable.}


(just suggested above) for stretching helical into stretched form of dsDNA
, how this protocol can be modified.


pull_ngroups   = 2
pull_ncoords   = 1
pull_group1_name= r_24 ; 3' of  chain B of dsDNA as a
reference gorup (not  fixed)
pull_group2_name= r_12  ;  3' of  chain A of dsDNA as a
pulling gorup
pull_coord1_type  = umbrella  ; harmonic biasing force
pull_coord1_geometry   = distance  ; simple distance increase
pull_coord1_groups   = 1  2
pull_coord1_dim   = Y  N  N
pull_coord1_rate  = 0.005  ; 0.005 nm per ps = 5nm per 1 ns
pull_coord1_k  = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start = yes   ; define initial COM distance > 0


And other question for which I really bother is that how it is possible to
apply this pull protocol of gromacs
in order to pull two gorups in apposite direction along the pulling
direction. Hoping for response

-- 

*With Best-Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +918777496532*
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 9/23/18 12:11 PM, AKANXA TIWARI wrote:

Hi
During simulation of protein after giving grompp ions command i got a note
what should i do.
  NOTE 3 [file ions2.mdp]:
   You are using a plain Coulomb cut-off, which might produce artifacts.
   You might want to consider using PME electrostatics.


This note is harmless if the .tpr file is only being used to add ions. 
Trying to use PME (e.g. by copying an .mdp file that is used for EM or 
MD) will trigger a fatal error due to the non-zero charge of the system. 
So .mdp files specifying plain cutoffs are necessary for adding ions, 
but should not be used for anything else.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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Re: [gmx-users] (no subject)

[Bratin Kumar Das]

In your .mdp file ...in cut-off you mention PME...

On Sun, Sep 23, 2018, 9:42 PM AKANXA TIWARI 
wrote:

> Hi
> During simulation of protein after giving grompp ions command i got a note
> what should i do.
>  NOTE 3 [file ions2.mdp]:
>   You are using a plain Coulomb cut-off, which might produce artifacts.
>   You might want to consider using PME electrostatics.
> --
> Gromacs Users mailing list
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> posting!
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[gmx-users] (no subject)

[AKANXA TIWARI]

Hi
During simulation of protein after giving grompp ions command i got a note
what should i do.
 NOTE 3 [file ions2.mdp]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.
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Re: [gmx-users] (no subject)

[Vytautas Rakeviius]

 I suggest this tool:https://github.com/llazzaro/acpype 

On Friday, September 14, 2018, 10:44:56 PM GMT+3, SAKO MIRZAIE 
 wrote:  
 
 Hi every one,
I need the topology parameters for pyridoxal phosphate linked to lysine
with amber99sb force field. does anyone have the mentioned parameters? I
searched it among publications but I didn't find it at all.

Best regards,

-- 
***
Sako Mirzaie
Ph.D. in biochemistry, Assistant Professor, Science Faculty, Islamic Azad
University of Sanandaj, Sanandaj, Iran

http://www.iausdj.ac.ir/_Academician?username=sakomirzaie

http://www.iausdj.ac.ir/_Academician/English?username=sakomirzaie

http://scholar.google.com/citations?user=viwZvVAJ=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
https://www.researchgate.net/profile/Sako_Mirzaie/publications/
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[gmx-users] (no subject)

[SAKO MIRZAIE]

Hi every one,
I need the topology parameters for pyridoxal phosphate linked to lysine
with amber99sb force field. does anyone have the mentioned parameters? I
searched it among publications but I didn't find it at all.

Best regards,

-- 
***
Sako Mirzaie
Ph.D. in biochemistry, Assistant Professor, Science Faculty, Islamic Azad
University of Sanandaj, Sanandaj, Iran

http://www.iausdj.ac.ir/_Academician?username=sakomirzaie

http://www.iausdj.ac.ir/_Academician/English?username=sakomirzaie

http://scholar.google.com/citations?user=viwZvVAJ=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
https://www.researchgate.net/profile/Sako_Mirzaie/publications/
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Re: [gmx-users] (no subject)

[AKANXA TIWARI]

thanks for reply


On Fri, Sep 14, 2018 at 5:09 PM Justin Lemkul  wrote:

>
>
> On 9/14/18 6:48 AM, AKANXA TIWARI wrote:
> > i am getting a warning after converting pdb2gmx and then applying force
> > field what i will do. please help me.i get this on screen.
> > WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was
> > mapped
> > to an entry in the topology database, but the atom H used in
> > an interaction of type angle in that entry is not found in the
> > input file. Perhaps your atom and/or residue naming needs to be
> > fixed.
> >
> >
> >
> > WARNING: WARNING: Residue 374 named PHE of a molecule in the input file
> was
> > mapped
> > to an entry in the topology database, but the atom O used in
> > an interaction of type angle in that entry is not found in the
> > input file. Perhaps your atom and/or residue naming needs to be
> > fixed.
> >
>
> pdb2gmx is just being a bit too noisy here. Termini are being patched,
> which means some atoms get deleted, replaced, or added. Here, an
> existing atom is being deleted and replaced with another at both the N-
> and C-termini. There is no problem, as you see the message below about
> successful completion.
>
> -Justin
>
> > Before cleaning: 6050 pairs
> > Before cleaning: 7868 dihedrals
> > Making cmap torsions...
> > There are 2709 dihedrals, 1833 impropers, 5404 angles
> >6050 pairs, 3705 bonds and 0 virtual sites
> > Total mass 40604.576 a.m.u.
> > Total charge 11.000 e
> > Writing topology
> >
> > Back Off! I just backed up posre.itp to ./#posre.itp.1#
> >
> > Writing coordinate file...
> >
> > Back Off! I just backed up actin_asp_processed.gro to
> > ./#actin_asp_processed.gro.1#
> >  - PLEASE NOTE 
> > You have successfully generated a topology from: actin_asp_clean.pdb.
> > The Gromos54a7 force field and the spce water model are used.
> >  - ETON ESAELP 
> >
> > GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross)
> >
> > akanxa@akanxa-HP-Notebook:~/Documents/aasp$
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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
>
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 9/14/18 6:48 AM, AKANXA TIWARI wrote:

i am getting a warning after converting pdb2gmx and then applying force
field what i will do. please help me.i get this on screen.
WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



WARNING: WARNING: Residue 374 named PHE of a molecule in the input file was
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



pdb2gmx is just being a bit too noisy here. Termini are being patched, 
which means some atoms get deleted, replaced, or added. Here, an 
existing atom is being deleted and replaced with another at both the N- 
and C-termini. There is no problem, as you see the message below about 
successful completion.


-Justin


Before cleaning: 6050 pairs
Before cleaning: 7868 dihedrals
Making cmap torsions...
There are 2709 dihedrals, 1833 impropers, 5404 angles
   6050 pairs, 3705 bonds and 0 virtual sites
Total mass 40604.576 a.m.u.
Total charge 11.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.1#

Writing coordinate file...

Back Off! I just backed up actin_asp_processed.gro to
./#actin_asp_processed.gro.1#
 - PLEASE NOTE 
You have successfully generated a topology from: actin_asp_clean.pdb.
The Gromos54a7 force field and the spce water model are used.
 - ETON ESAELP 

GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross)

akanxa@akanxa-HP-Notebook:~/Documents/aasp$


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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Re: [gmx-users] (no subject)

[Bratin Kumar Das]

You need to add the particular H to the amino acid .rtp file in the
forcefield folder

On Fri, Sep 14, 2018, 4:24 PM AKANXA TIWARI 
wrote:

> i am getting a warning after converting pdb2gmx and then applying force
> field what i will do. please help me.i get this on screen.
> WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom H used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
>
> WARNING: WARNING: Residue 374 named PHE of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom O used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
> Before cleaning: 6050 pairs
> Before cleaning: 7868 dihedrals
> Making cmap torsions...
> There are 2709 dihedrals, 1833 impropers, 5404 angles
>   6050 pairs, 3705 bonds and 0 virtual sites
> Total mass 40604.576 a.m.u.
> Total charge 11.000 e
> Writing topology
>
> Back Off! I just backed up posre.itp to ./#posre.itp.1#
>
> Writing coordinate file...
>
> Back Off! I just backed up actin_asp_processed.gro to
> ./#actin_asp_processed.gro.1#
> - PLEASE NOTE 
> You have successfully generated a topology from: actin_asp_clean.pdb.
> The Gromos54a7 force field and the spce water model are used.
> - ETON ESAELP 
>
> GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross)
>
> akanxa@akanxa-HP-Notebook:~/Documents/aasp$
> --
> 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.
>
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[gmx-users] (no subject)

[AKANXA TIWARI]

i am getting a warning after converting pdb2gmx and then applying force
field what i will do. please help me.i get this on screen.
WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



WARNING: WARNING: Residue 374 named PHE of a molecule in the input file was
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.


Before cleaning: 6050 pairs
Before cleaning: 7868 dihedrals
Making cmap torsions...
There are 2709 dihedrals, 1833 impropers, 5404 angles
  6050 pairs, 3705 bonds and 0 virtual sites
Total mass 40604.576 a.m.u.
Total charge 11.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.1#

Writing coordinate file...

Back Off! I just backed up actin_asp_processed.gro to
./#actin_asp_processed.gro.1#
- PLEASE NOTE 
You have successfully generated a topology from: actin_asp_clean.pdb.
The Gromos54a7 force field and the spce water model are used.
- ETON ESAELP 

GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross)

akanxa@akanxa-HP-Notebook:~/Documents/aasp$
-- 
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 9/10/18 9:14 AM, Bratin Kumar Das wrote:

Use -maxwarn 2 at the last of your gmx grompp ... command


No! One should *never* use -maxwarn just to circumvent problems. It is 
clear that there is some modification to ffnonbonded.itp that is 
syntactically incorrect. grompp will not have the right parameters and 
any process that tries to use this .tpr file will fail.


-Justin


On Mon, Sep 10, 2018, 6:19 PM saranya  wrote:


Dear Users,

 My simulation system is Amyloid β Protein (1-42) with Fe2+ complex
and i am using OPLSAA forcefield for the simulations. I edited the
ffbonded.itp files accordingly as mentioned in the tutorials.

While running grompp command, I get following error:



gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr

   :-) GROMACS - gmx grompp, VERSION 5.1.2 (-:



 GROMACS is written by:

  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar

  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch

   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
Hindriksen

  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner

 Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff

Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk

Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers

Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf

and the project leaders:

 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel



Copyright (c) 1991-2000, University of Groningen, The Netherlands.

Copyright (c) 2001-2015, The GROMACS development team at

Uppsala University, Stockholm University and

the Royal Institute of Technology, Sweden.

check out http://www.gromacs.org for more information.



GROMACS is free software; you can redistribute it and/or modify it

under the terms of the GNU Lesser General Public License

as published by the Free Software Foundation; either version 2.1

of the License, or (at your option) any later version.



GROMACS:  gmx grompp, VERSION 5.1.2

Executable:   /usr/local/gromacs/bin/gmx

Data prefix:  /usr/local/gromacs

Command line:

   gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr



Ignoring obsolete mdp entry 'title'



Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

Setting the LD random seed to 2295799000



WARNING 1 [file ffnonbonded.itp, line 3]:

   Too few parameters on line (source file

   /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c,

   line 283)



Generated 335790 of the 335790 non-bonded parameter combinations

Generating 1-4 interactions: fudge = 0.5

Generated 335790 of the 335790 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type 'Protein_chain_A'

Excluding 2 bonded neighbours molecule type 'SOL'



NOTE 1 [file c5.top, line 5912]:

   System has non-zero total charge: -2.00

   Total charge should normally be an integer. See

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

   for discussion on how close it should be to an integer.







Removing all charge groups because cutoff-scheme=Verlet

Analysing residue names:

There are:42Protein residues

There are: 1  Other residues

There are:  8015  Water residues

Analysing Protein...

Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...

Number of degrees of freedom in T-Coupling group rest is 49971.00

Calculating fourier grid dimensions for X Y Z

Using a fourier grid of 56x56x56, spacing 0.113 0.113 0.113

Estimate for the relative computational load of the PME mesh part: 0.23

This run will generate roughly 2 Mb of data



There was 1 note



There was 1 warning



---

Program gmx grompp, VERSION 5.1.2

Source code file:
/home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c,
line: 2107



Fatal error:

Too many warnings (1), gmx terminated.

If you are sure all warnings are harmless, use the -maxwarn option.

For more information and tips for troubleshooting, please check the GROMACS

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

---



Anyone can help me in overcoming this fatal error will be appreciated.





With Regards,

Saranya Vasudevan,

Research Scholar,

Molecular Quantum Mechanics Laboratory,

Department of Physics,

Bharathiar University,

Coimbatore-46
--
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

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send a mail to gmx-users-requ...@gromacs.org.


--

Re: [gmx-users] (no subject)

[Bratin Kumar Das]

Use -maxwarn 2 at the last of your gmx grompp ... command

On Mon, Sep 10, 2018, 6:19 PM saranya  wrote:

> Dear Users,
>
> My simulation system is Amyloid β Protein (1-42) with Fe2+ complex
> and i am using OPLSAA forcefield for the simulations. I edited the
> ffbonded.itp files accordingly as mentioned in the tutorials.
>
> While running grompp command, I get following error:
>
>
>
> gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr
>
>   :-) GROMACS - gmx grompp, VERSION 5.1.2 (-:
>
>
>
> GROMACS is written by:
>
>  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> Bjelkmar
>
>  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
>
>   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
> Hindriksen
>
>  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner
>
> Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
>
>Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
>
>Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
>
>Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
>
>and the project leaders:
>
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
>
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>
> Copyright (c) 2001-2015, The GROMACS development team at
>
> Uppsala University, Stockholm University and
>
> the Royal Institute of Technology, Sweden.
>
> check out http://www.gromacs.org for more information.
>
>
>
> GROMACS is free software; you can redistribute it and/or modify it
>
> under the terms of the GNU Lesser General Public License
>
> as published by the Free Software Foundation; either version 2.1
>
> of the License, or (at your option) any later version.
>
>
>
> GROMACS:  gmx grompp, VERSION 5.1.2
>
> Executable:   /usr/local/gromacs/bin/gmx
>
> Data prefix:  /usr/local/gromacs
>
> Command line:
>
>   gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr
>
>
>
> Ignoring obsolete mdp entry 'title'
>
>
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
>
> Setting the LD random seed to 2295799000
>
>
>
> WARNING 1 [file ffnonbonded.itp, line 3]:
>
>   Too few parameters on line (source file
>
>   /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c,
>
>   line 283)
>
>
>
> Generated 335790 of the 335790 non-bonded parameter combinations
>
> Generating 1-4 interactions: fudge = 0.5
>
> Generated 335790 of the 335790 1-4 parameter combinations
>
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
>
> Excluding 2 bonded neighbours molecule type 'SOL'
>
>
>
> NOTE 1 [file c5.top, line 5912]:
>
>   System has non-zero total charge: -2.00
>
>   Total charge should normally be an integer. See
>
>   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>
>   for discussion on how close it should be to an integer.
>
>
>
>
>
>
>
> Removing all charge groups because cutoff-scheme=Verlet
>
> Analysing residue names:
>
> There are:42Protein residues
>
> There are: 1  Other residues
>
> There are:  8015  Water residues
>
> Analysing Protein...
>
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
>
> Number of degrees of freedom in T-Coupling group rest is 49971.00
>
> Calculating fourier grid dimensions for X Y Z
>
> Using a fourier grid of 56x56x56, spacing 0.113 0.113 0.113
>
> Estimate for the relative computational load of the PME mesh part: 0.23
>
> This run will generate roughly 2 Mb of data
>
>
>
> There was 1 note
>
>
>
> There was 1 warning
>
>
>
> ---
>
> Program gmx grompp, VERSION 5.1.2
>
> Source code file:
> /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c,
> line: 2107
>
>
>
> Fatal error:
>
> Too many warnings (1), gmx terminated.
>
> If you are sure all warnings are harmless, use the -maxwarn option.
>
> For more information and tips for troubleshooting, please check the GROMACS
>
> website at http://www.gromacs.org/Documentation/Errors
>
> ---
>
>
>
> Anyone can help me in overcoming this fatal error will be appreciated.
>
>
>
>
>
> With Regards,
>
> Saranya Vasudevan,
>
> Research Scholar,
>
> Molecular Quantum Mechanics Laboratory,
>
> Department of Physics,
>
> Bharathiar University,
>
> Coimbatore-46
> --
> 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] (no subject)

[saranya]

Dear Users,

My simulation system is Amyloid β Protein (1-42) with Fe2+ complex
and i am using OPLSAA forcefield for the simulations. I edited the
ffbonded.itp files accordingly as mentioned in the tutorials.

While running grompp command, I get following error:



gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr

  :-) GROMACS - gmx grompp, VERSION 5.1.2 (-:



GROMACS is written by:

 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar

 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch

  Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen

 Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner

Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff

   Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk

   Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers

   Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf

   and the project leaders:

Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel



Copyright (c) 1991-2000, University of Groningen, The Netherlands.

Copyright (c) 2001-2015, The GROMACS development team at

Uppsala University, Stockholm University and

the Royal Institute of Technology, Sweden.

check out http://www.gromacs.org for more information.



GROMACS is free software; you can redistribute it and/or modify it

under the terms of the GNU Lesser General Public License

as published by the Free Software Foundation; either version 2.1

of the License, or (at your option) any later version.



GROMACS:  gmx grompp, VERSION 5.1.2

Executable:   /usr/local/gromacs/bin/gmx

Data prefix:  /usr/local/gromacs

Command line:

  gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr



Ignoring obsolete mdp entry 'title'



Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

Setting the LD random seed to 2295799000



WARNING 1 [file ffnonbonded.itp, line 3]:

  Too few parameters on line (source file

  /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c,

  line 283)



Generated 335790 of the 335790 non-bonded parameter combinations

Generating 1-4 interactions: fudge = 0.5

Generated 335790 of the 335790 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type 'Protein_chain_A'

Excluding 2 bonded neighbours molecule type 'SOL'



NOTE 1 [file c5.top, line 5912]:

  System has non-zero total charge: -2.00

  Total charge should normally be an integer. See

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

  for discussion on how close it should be to an integer.







Removing all charge groups because cutoff-scheme=Verlet

Analysing residue names:

There are:42Protein residues

There are: 1  Other residues

There are:  8015  Water residues

Analysing Protein...

Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...

Number of degrees of freedom in T-Coupling group rest is 49971.00

Calculating fourier grid dimensions for X Y Z

Using a fourier grid of 56x56x56, spacing 0.113 0.113 0.113

Estimate for the relative computational load of the PME mesh part: 0.23

This run will generate roughly 2 Mb of data



There was 1 note



There was 1 warning



---

Program gmx grompp, VERSION 5.1.2

Source code file:
/home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c,
line: 2107



Fatal error:

Too many warnings (1), gmx terminated.

If you are sure all warnings are harmless, use the -maxwarn option.

For more information and tips for troubleshooting, please check the GROMACS

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

---



Anyone can help me in overcoming this fatal error will be appreciated.





With Regards,

Saranya Vasudevan,

Research Scholar,

Molecular Quantum Mechanics Laboratory,

Department of Physics,

Bharathiar University,

Coimbatore-46
-- 
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] (no subject)

[Rakesh Mishra]

Dear  Mark,

I think things are not under solution.

Please tell me if there is  dsDNA of chain A (12 bp)
and  complimentary strand B(12 bp)  like

chain A-   3' - 5'
chain B-   5' - 3'
I am pulling   5' end  of strand  A and made 5' of B as a reference group
along the helical direction under constant velocity pulling. And both the
chains are free ( no restraint) ,
under this situation will the 5' of chain B (act as reference group) feel
the equal and opposite force like 5' end of chain A where pulling is
applied .
Due to this equal and opposite force both the strand will move opposite to
each other or not .



On Mon, Sep 3, 2018 at 10:00 AM, Rakesh Mishra  wrote:

> Hi Mark
>
> Did you get the point or  not .
> Hoping your  response
>
> On Fri, Aug 31, 2018 at 6:17 PM, Rakesh Mishra 
> wrote:
>
>>
>> *Please remember (its your  query to me )*
>> Hi,
>>
>> Can you please share a link to something that indicates why this would be
>> a
>> good tool for modeling such experimental pulling scenarios? Making the
>> case
>> for implementing such a feature would benefit from that.
>>
>> Mark
>> > > dt)+-+t2,+e=gmail=g
>> 
>> >
>>
>>
>>
>> *This is our response *
>>
>>
>> Dear Mark,
>>
>> There are several experiments have been done for protein and DNA
>> unfolding.
>> Thy  became pioneer in this field.  That is why force should apply and
>> corresponding reaction
>> coordinates are measured . Here Gromacs login do not allow to upload
>> larger data.
>> But I can mention some paper address . If get time Please go through
>> these papers .
>>
>> 1- NATURE | VOL 421 | 23 JANUARY 2003 | www.nature.com/nature (Carlos
>> Bustamante*†, Zev Bryant* & Steven B. Smith†)
>>
>> 2-  SCIENCE 1⁄7 VOL. 275 1⁄7 28 FEBRUARY 1997 (Matthias Rief, Filipp
>> Oesterhelt, Berthold Heymann,Hermann E. Gaub )
>>
>> That is  why I  asked about force-extension protocol.  In Umbrella
>> sampling distance is increases linearly with the time and corresponding
>> force experienced by the system writes .
>>
>> We still don't no that force/time which writes in .xvg file corresponds
>> which formula like f= k(vt-x) or something else.
>> There are other lot experiments regarding measurement of stability of the
>> DNA and protein under f/x curve.
>> One can see some theory paper also to see f/x like.
>>
>> 1- THE JOURNAL OF CHEMICAL PHYSICS 148, 215105 (2018)
>>
>>
>>
>>
>> Note- According to Justin one  can write that protocol. If suppose we
>> write that protocol, then how  to apply in gromacs.
>>
>> There are only input .mdp files. We didn't know  where to built the force
>> subroutine in .ff (force field ) directory. or somewhere else.
>>
>>
>> Hoping for  response.
>>
>>
>>
>>
>>
>>
>> On Fri, Aug 31, 2018 at 6:08 PM, Rakesh Mishra 
>> wrote:
>>
>>> Dear  mark
>>> I had already discussed regarding force/extension protocol.
>>> But I didn't get any response from your side. I dont have
>>> idea to upload some pictures.
>>>
>>> On Fri, Aug 31, 2018 at 4:05 PM, Mark Abraham 
>>> wrote:
>>>
 Hi,

 The list cannot accept attachments. Upload to a file sharing service and
 share a link. We will likely need more background information also.

 Mark

 On Fri, Aug 31, 2018, 12:22 Rakesh Mishra  wrote:

 > Hi every body
 > can any one  explain what is the mean of this graph
 > obtained from gromacs  constant velocity pulling of dsDNA
 > along the helical direction. (force.xvg). Basically sudden drop of
 force
 > represents what ?
 > --
 > 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.

>>>
>>>
>>>
>>> --
>>>
>>> *With Best-Rakesh Kumar Mishra*
>>> *  (RA)CSD  SINP Kolkata, India*
>>>
>>> *E-mail - rakesh.mis...@saha.ac.in  *
>>>
>>> *Phone n. +91 9473662491, +918777496532*
>>>
>>
>>
>>
>> --
>>
>> *With Best-Rakesh Kumar Mishra*
>> *  (RA)CSD  SINP Kolkata, India*
>>
>> *E-mail - rakesh.mis...@saha.ac.in  *
>>
>> *Phone n. +91 9473662491, +918777496532*
>>
>
>
>
> --
>
> *With Best-Rakesh Kumar Mishra*
> *  (RA)CSD  SINP Kolkata, India*
>
> *E-mail - rakesh.mis...@saha.ac.in  *

Re: [gmx-users] (no subject)

[Rakesh Mishra]

Hi Mark

Did you get the point or  not .
Hoping your  response

On Fri, Aug 31, 2018 at 6:17 PM, Rakesh Mishra  wrote:

>
> *Please remember (its your  query to me )*
> Hi,
>
> Can you please share a link to something that indicates why this would be a
> good tool for modeling such experimental pulling scenarios? Making the case
> for implementing such a feature would benefit from that.
>
> Mark
> >  dt)+-+t2,+e=gmail=g
> 
> >
>
>
>
> *This is our response *
>
>
> Dear Mark,
>
> There are several experiments have been done for protein and DNA
> unfolding.
> Thy  became pioneer in this field.  That is why force should apply and
> corresponding reaction
> coordinates are measured . Here Gromacs login do not allow to upload
> larger data.
> But I can mention some paper address . If get time Please go through these
> papers .
>
> 1- NATURE | VOL 421 | 23 JANUARY 2003 | www.nature.com/nature (Carlos
> Bustamante*†, Zev Bryant* & Steven B. Smith†)
>
> 2-  SCIENCE 1⁄7 VOL. 275 1⁄7 28 FEBRUARY 1997 (Matthias Rief, Filipp
> Oesterhelt, Berthold Heymann,Hermann E. Gaub )
>
> That is  why I  asked about force-extension protocol.  In Umbrella
> sampling distance is increases linearly with the time and corresponding
> force experienced by the system writes .
>
> We still don't no that force/time which writes in .xvg file corresponds
> which formula like f= k(vt-x) or something else.
> There are other lot experiments regarding measurement of stability of the
> DNA and protein under f/x curve.
> One can see some theory paper also to see f/x like.
>
> 1- THE JOURNAL OF CHEMICAL PHYSICS 148, 215105 (2018)
>
>
>
>
> Note- According to Justin one  can write that protocol. If suppose we
> write that protocol, then how  to apply in gromacs.
>
> There are only input .mdp files. We didn't know  where to built the force
> subroutine in .ff (force field ) directory. or somewhere else.
>
>
> Hoping for  response.
>
>
>
>
>
>
> On Fri, Aug 31, 2018 at 6:08 PM, Rakesh Mishra 
> wrote:
>
>> Dear  mark
>> I had already discussed regarding force/extension protocol.
>> But I didn't get any response from your side. I dont have
>> idea to upload some pictures.
>>
>> On Fri, Aug 31, 2018 at 4:05 PM, Mark Abraham 
>> wrote:
>>
>>> Hi,
>>>
>>> The list cannot accept attachments. Upload to a file sharing service and
>>> share a link. We will likely need more background information also.
>>>
>>> Mark
>>>
>>> On Fri, Aug 31, 2018, 12:22 Rakesh Mishra  wrote:
>>>
>>> > Hi every body
>>> > can any one  explain what is the mean of this graph
>>> > obtained from gromacs  constant velocity pulling of dsDNA
>>> > along the helical direction. (force.xvg). Basically sudden drop of
>>> force
>>> > represents what ?
>>> > --
>>> > 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.
>>>
>>
>>
>>
>> --
>>
>> *With Best-Rakesh Kumar Mishra*
>> *  (RA)CSD  SINP Kolkata, India*
>>
>> *E-mail - rakesh.mis...@saha.ac.in  *
>>
>> *Phone n. +91 9473662491, +918777496532*
>>
>
>
>
> --
>
> *With Best-Rakesh Kumar Mishra*
> *  (RA)CSD  SINP Kolkata, India*
>
> *E-mail - rakesh.mis...@saha.ac.in  *
>
> *Phone n. +91 9473662491, +918777496532*
>



-- 

*With Best-Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +918777496532*
-- 
Gromacs Users mailing list

* Please search the archive at 
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* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.