Re: [gmx-users] Angle between two plane

[NOKK SIEMPRE]

Please see gmx sorient command from the manual.
Regards
Nabin

El mié., 12 sept. 2018 a las 9:23, rose rahmani ()
escribió:

> Hi,
>
> Hiw can i calculate angle between two plane?(HOH plane of water and surface
> plane or perpendicular axis to it? How should i make an index for defining
> HOH plane?
>
> Best
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Re: [gmx-users] Make check failed 2018 Gromacs on GPU workstation

[Szilárd Páll]

Test timeouts are strange, Is the machine you're running on busy with other
jobs?

Regarding the regressiontest failure, can you share
tests/regressiontests*/complex/octahedron/mdrun.out
please?

--
Szilárd


On Thu, Sep 13, 2018 at 8:49 PM Phuong Tran  wrote:

> Hi all,
>
> I have been trying to install Gromacs on our GPU workstation that has CUDA
> 9.0
> It went well but 'make check' have failed so far on either 2018.3 or 2018.2
> versions.
> anybody know how to resolve it?
> Please see the error below.
> Thank you,
> -T
>
> Test project /home/user/Softwares/gromacs-2018.3/build
>
> .
>
>
>  9/39 Test  #9: GpuUtilsUnitTests ***Timeout  30.35 sec
>
>
> .
>
>
> 35/39 Test #35: regressiontests/complex ..***Failed  174.98 sec
>
>
>
> GROMACS:  gmx mdrun, version 2018.3
>
> Executable:   /home/user/Softwares/gromacs-2018.3/build/bin/gmx
>
> Data prefix:  /home/user/Softwares/gromacs-2018.3 (source tree)
>
> Working dir:
> /home/user/Softwares/gromacs-2018.3/build/tests/regressiontests-2018.3
>
> Command line:
>
>   gmx mdrun -h
>
>
>
> Thanx for Using GROMACS - Have a Nice Day
>
>
> Mdrun cannot use the requested (or automatic) number of ranks, retrying
> with 8.
>
>
> Abnormal return value for ' gmx mdrun-nb cpu   -notunepme >mdrun.out
> 2>&1' was 1
>
> Retrying mdrun with better settings...
>
>
> Abnormal return value for ' gmx mdrun   -notunepme >mdrun.out 2>&1' was
> -1
>
> FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron
>
> Re-running orientation-restraints using CPU-based PME
>
> Re-running pull_geometry_angle using CPU-based PME
>
> Re-running pull_geometry_angle-axis using CPU-based PME
>
> Re-running pull_geometry_dihedral using CPU-based PME
>
> 1 out of 55 complex tests FAILED
>
>
>  
>
>
> 95% tests passed, 2 tests failed out of 39
>
>
> Label Time Summary:
>
> GTest  = 133.55 sec (33 tests)
>
> IntegrationTest=  88.38 sec (3 tests)
>
> MpiTest=   2.82 sec (3 tests)
>
> UnitTest   =  45.17 sec (30 tests)
>
>
> Total Test time (real) = 810.78 sec
>
>
> The following tests FAILED:
>
>   9 - GpuUtilsUnitTests (Timeout)
>
>  35 - regressiontests/complex (Failed)
>
> Errors while running CTest
>
> CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
> 'CMakeFiles/run-ctest-nophys' failed
>
> make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
>
> CMakeFiles/Makefile2:1160: recipe for target
> 'CMakeFiles/run-ctest-nophys.dir/all' failed
>
> make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
>
> CMakeFiles/Makefile2:971: recipe for target 'CMakeFiles/check.dir/rule'
> failed
>
> make[1]: *** [CMakeFiles/check.dir/rule] Error 2
>
> Makefile:546: recipe for target 'check' failed
>
> make: *** [check] Error 2
> ReplyForward
> 
> 
> 
> 
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Re: [gmx-users] TAU-P

[Alex]

Hi Justin,
Any comment please one the initial question of the current ticket?

Thanks.
Alex

On Thu, Sep 13, 2018 at 5:04 PM Justin Lemkul  wrote:

>
>
> On 9/13/18 4:34 PM, Huang, Tina wrote:
> > How do I unsubscribe? :)
>
> In the footer of every email across the list:
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users  or
> send a mail togmx-users-requ...@gromacs.org.
>
> -Justin
>
>
>
> >
> > Thanks!
> > Tina
> >
> > On Thu, Sep 13, 2018 at 10:45 AM, Alex 
> wrote:
> >
> >> Dear all,
> >> I wonder how tau-p/tau-t can affect on simulation and how it should be
> >> chosen wisely according to the system of study?
> >>
> >> Also, the performance of GMX-2018.2 is around 10 ns/day for NVT/NpT
> >> equilibration of a system while the performance increases to around 18
> >> ns/day for the NVT production simulation of the same system. Do you
> think
> >> the only reason for the difference is that I use dt = 0.001 for
> >> equilibration
> >> but dt = 0.002 for the production? or something else might also play
> role?
> >>
> >> Thank you.
> >> Alex
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/
> >> Support/Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
>
> --
> ==
>
> 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] TAU-P

[Justin Lemkul]

On 9/13/18 4:34 PM, Huang, Tina wrote:

How do I unsubscribe? :)


In the footer of every email across the list:

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users  or
send a mail togmx-users-requ...@gromacs.org.

-Justin





Thanks!
Tina

On Thu, Sep 13, 2018 at 10:45 AM, Alex  wrote:


Dear all,
I wonder how tau-p/tau-t can affect on simulation and how it should be
chosen wisely according to the system of study?

Also, the performance of GMX-2018.2 is around 10 ns/day for NVT/NpT
equilibration of a system while the performance increases to around 18
ns/day for the NVT production simulation of the same system. Do you think
the only reason for the difference is that I use dt = 0.001 for
equilibration
but dt = 0.002 for the production? or something else might also play role?

Thank you.
Alex
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--
==

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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] TAU-P

[Huang, Tina]

How do I unsubscribe? :)

Thanks!
Tina

On Thu, Sep 13, 2018 at 10:45 AM, Alex  wrote:

> Dear all,
> I wonder how tau-p/tau-t can affect on simulation and how it should be
> chosen wisely according to the system of study?
>
> Also, the performance of GMX-2018.2 is around 10 ns/day for NVT/NpT
> equilibration of a system while the performance increases to around 18
> ns/day for the NVT production simulation of the same system. Do you think
> the only reason for the difference is that I use dt = 0.001 for
> equilibration
> but dt = 0.002 for the production? or something else might also play role?
>
> Thank you.
> Alex
> --
> Gromacs Users mailing list
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[gmx-users] Make check failed 2018 Gromacs on GPU workstation

[Phuong Tran]

Hi all,

I have been trying to install Gromacs on our GPU workstation that has CUDA
9.0
It went well but 'make check' have failed so far on either 2018.3 or 2018.2
versions.
anybody know how to resolve it?
Please see the error below.
Thank you,
-T

Test project /home/user/Softwares/gromacs-2018.3/build

.


 9/39 Test  #9: GpuUtilsUnitTests ***Timeout  30.35 sec


.


35/39 Test #35: regressiontests/complex ..***Failed  174.98 sec



GROMACS:  gmx mdrun, version 2018.3

Executable:   /home/user/Softwares/gromacs-2018.3/build/bin/gmx

Data prefix:  /home/user/Softwares/gromacs-2018.3 (source tree)

Working dir:
/home/user/Softwares/gromacs-2018.3/build/tests/regressiontests-2018.3

Command line:

  gmx mdrun -h



Thanx for Using GROMACS - Have a Nice Day


Mdrun cannot use the requested (or automatic) number of ranks, retrying
with 8.


Abnormal return value for ' gmx mdrun-nb cpu   -notunepme >mdrun.out
2>&1' was 1

Retrying mdrun with better settings...


Abnormal return value for ' gmx mdrun   -notunepme >mdrun.out 2>&1' was
-1

FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron

Re-running orientation-restraints using CPU-based PME

Re-running pull_geometry_angle using CPU-based PME

Re-running pull_geometry_angle-axis using CPU-based PME

Re-running pull_geometry_dihedral using CPU-based PME

1 out of 55 complex tests FAILED


 


95% tests passed, 2 tests failed out of 39


Label Time Summary:

GTest  = 133.55 sec (33 tests)

IntegrationTest=  88.38 sec (3 tests)

MpiTest=   2.82 sec (3 tests)

UnitTest   =  45.17 sec (30 tests)


Total Test time (real) = 810.78 sec


The following tests FAILED:

  9 - GpuUtilsUnitTests (Timeout)

 35 - regressiontests/complex (Failed)

Errors while running CTest

CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
'CMakeFiles/run-ctest-nophys' failed

make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8

CMakeFiles/Makefile2:1160: recipe for target
'CMakeFiles/run-ctest-nophys.dir/all' failed

make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2

CMakeFiles/Makefile2:971: recipe for target 'CMakeFiles/check.dir/rule'
failed

make[1]: *** [CMakeFiles/check.dir/rule] Error 2

Makefile:546: recipe for target 'check' failed

make: *** [check] Error 2
ReplyForward




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[gmx-users] TAU-P

[Alex]

Dear all,
I wonder how tau-p/tau-t can affect on simulation and how it should be
chosen wisely according to the system of study?

Also, the performance of GMX-2018.2 is around 10 ns/day for NVT/NpT
equilibration of a system while the performance increases to around 18
ns/day for the NVT production simulation of the same system. Do you think
the only reason for the difference is that I use dt = 0.001 for equilibration
but dt = 0.002 for the production? or something else might also play role?

Thank you.
Alex
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[gmx-users] Population Density Plot

[ISHRAT JAHAN]

Dear all,
Can anyone tell me the command used for calculating the population density
plot between Ree and Rg? As I have calculated the Ree and Rg value from gmx
polystat command now, i want to plot population density between Ree and Rg.
Your help will be appreciated.
Thank u
-
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh
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Re: [gmx-users] Your message to gromacs.org_gmx-users awaits moderator approval

[Nick Johans]

Thank you dear justin, finally you answer me;)

On Thu, 13 Sep 2018, 16:59 Justin Lemkul,  wrote:

>
>
> On 9/13/18 7:55 AM, rose rahmani wrote:
> > Hi,
> >
> > I recieved an email from GROMACS, says the message is too big(because of
> > many replies). So what should i do to continue my discussion?
>
> Cut out old, unimportant text.
>
> -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] Your message to gromacs.org_gmx-users awaits moderator approval

[Justin Lemkul]

On 9/13/18 7:55 AM, rose rahmani wrote:

Hi,

I recieved an email from GROMACS, says the message is too big(because of
many replies). So what should i do to continue my discussion?


Cut out old, unimportant text.

-Justin

--
==

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

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

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

==

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[gmx-users] Your message to gromacs.org_gmx-users awaits moderator approval

[rose rahmani]

Hi,

I recieved an email from GROMACS, says the message is too big(because of
many replies). So what should i do to continue my discussion?

Best
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Re: [gmx-users] Problem with mdrun and shell particles (polarizable ff)

[Justin Lemkul]

On 9/13/18 7:56 AM, Matteo Busato wrote:

Hi to everyone,


I am trying to perform a calculation on a cluster, where Gromacs 5.1.4 was 
compiled, using a polarizable force field carrying shells. Since domain 
decomposition can not be used, I was trying to launch mdrun with  the -ntmpi 1 
-ntomp=number-of-cores options as Justin stated in an old discussion 
(https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-September/092341.html).
 However, the program gives me this error:


Fatal error: "Setting the number of thread-MPI ranks is only supported with 
thread-MPI and GROMACS was compiled without thread-MPI".


Since I have not the superuser permission for this cluster, is there any 
solution that avoids recompiling Gromacs?


GROMACS needs to be compiled with thread-MPI support, and you can always 
install your own version of the code within your home directory without 
needing su.


-Justin

--
==

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

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

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

==

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[gmx-users] Problem with mdrun and shell particles (polarizable ff)

[Matteo Busato]

Hi to everyone,


I am trying to perform a calculation on a cluster, where Gromacs 5.1.4 was 
compiled, using a polarizable force field carrying shells. Since domain 
decomposition can not be used, I was trying to launch mdrun with  the -ntmpi 1 
-ntomp=number-of-cores options as Justin stated in an old discussion 
(https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-September/092341.html).
 However, the program gives me this error:


Fatal error: "Setting the number of thread-MPI ranks is only supported with 
thread-MPI and GROMACS was compiled without thread-MPI".


Since I have not the superuser permission for this cluster, is there any 
solution that avoids recompiling Gromacs?


Please tell me if any further information is needed.


Thank you in advance.

Regards,

Matteo


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Re: [gmx-users] Justin paper 2010 pulling

[Justin Lemkul]

On 9/13/18 1:20 AM, Rakesh Mishra wrote:

I do not believe .

Because if I run multiple simulation of pulling with the same system and
with the
same inputs then almost we are getting similar force/time curve.
While we are getting different curve if we are saving position coordinates
or energy
coordinates with different frequency.


There is no aspect of the code in which the computation of forces 
depends on output frequency. You're welcome to disbelieve me, but you're 
clearly just getting different simulation outcomes from different 
inputs, or there's something else that differs that you haven't realized 
or haven't told us.


-Justin


On Wed, Sep 12, 2018 at 8:15 PM, Justin Lemkul  wrote:



On 9/12/18 8:42 AM, Rakesh Mishra wrote:


Dear Justin

It is totally surprised for me.
   I am pulling the same system of bdna
with the same constant velocity (0.005nm/ps).

Case 1
let for first case, When I am saving position coordinate (nstxtc ) in the
interval of 4ps
and saving energy coordinate in the interval of 4ps.

Case 2
In the second case of pulling of the same system with the same velocity,
we
save position
coordinate in the interval of 4ps but we save energy coordinate in the
interval of  10ps.

Now in the output file of force.xvg for both case qualitative behaviour of
diagram is same but
Peak of the forces are much differ.  Why this saving frequency is
affecting
the peak value. While
it is just saving the coordinates.

We also found that, if we save energy coordinate with the same frequency
and position
coordinate with different frequency then, again peak value of forces are
different.
Which should not. Why it is happening. Can you clarify please.


Your results have nothing to do with the save frequency. The output in
pullf.xvg is specified by pull-nstfout, not any of the others. You have
different simulations that behave differently, because there are elements
of randomness in any MD simulation. Pulling is a non-equilibrium process;
you may have to run several times with different pull vectors to find the
minimum-energy path.

-Justin




On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul  wrote:



On 9/6/18 2:29 AM, Rakesh Mishra wrote:

While I have purely physics background.

But, In my thinking, there are hydrogen bonds (electrostatic attractive
interaction)
between bp of  both the strands of DNA/RNA  which are perpendicular to
helix direction.
And the other thing you have chosen very fast velocity like (0.01,
0.001,
0.005 ).
This can also be the reason of smoothness. But can you tell me one thing
please,the
value of spring constant of biasing that you have taken (k= 1000), is
standard or not . If this value can be taken for peptide pulling .  Can
this value of
spring constant (k=1000) can be taken  for DNA (or dna+drug) pulling or
not .

There is no such thing as a "standard" force constant for pulling.

-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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==

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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--
==

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] cgenff charm error

[Justin Lemkul]

On 9/13/18 6:17 AM, marzieh dehghan wrote:

Hi
Dear all
I used charm36 and cgenff (http://mackerell.umaryland.edu/charmm_ff.shtml)
to convert str format of ligand to itp format. when I used the following
command:

python cgenff_charmm2gmx.py LIG lig.mol2 lig.str charmm36-jul2017.ff/

I confront this error:


NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, Dec  4
2017, 14:50:18)
[GCC 5.4.0 20160609]

NOTE2: Please be sure to use the same version of CGenFF in your simulations
that was used during parameter generation:
Traceback (most recent call last):
   File "cgenff_charmm2gmx.py", line 777, in 
 check_versions(rtp_name,ffdir + "/forcefield.doc")
   File "cgenff_charmm2gmx.py", line 53, in check_versions
 f = open(str_filename, 'r')
IOError: [Errno 2] No such file or directory: 'LIG1.str'


The error is quite simple: LIG1.str does not exist in the working 
directory. This also means that what you posted above for your command 
is not at all what you actually typed. Please always copy and paste 
commands from your terminal rather than trying to re-create what you did.



I installed python 2.7.3 for ubuntu, but it seems that it has not been
installed.


You don't need Python 2.7.3; the script is merely advising you of what 
has been used for testing in the event that there is an actual 
Python-related issue.


-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] cgenff charm error

[LAM, Tsz Nok]

Hi Marzieh,

I don't think the error is related to python version, but the naming of the 
files. Maybe the script needs that your input files are also named as LIG.str 
and LIG.mol2, something like that.

What I do know about the script when using it before, is that it requires an 
older version of python package "networkx" (I tested that version 1.9 worked). 
If you see further errors, you may want to try pip and virtualenv to use the 
appropriate packages, e.g.:

$ sudo apt install virtualenv pip
$ virtualenv new_directory  # making virtualenv directory with tools inside
$ source virtual/bin/activate  #activating virtualenv
$ pip install network==1.9   #specify to use version 1.9
$ pip install numpy

Then your script should work fine (You can deactivate virtualenv afterwards). 
More on pip and virtualenv:
https://packaging.python.org/tutorials/installing-packages/#installing-from-pypi

Wish you luck!
Cheers,
LAM Tsz-Nok
School of Life Sciences, The Chinese University of Hong Kong

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of marzieh 
dehghan 
Sent: Thursday, September 13, 2018 6:17:09 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] cgenff charm error

Hi
Dear all
I used charm36 and cgenff (http://mackerell.umaryland.edu/charmm_ff.shtml)
to convert str format of ligand to itp format. when I used the following
command:

python cgenff_charmm2gmx.py LIG lig.mol2 lig.str charmm36-jul2017.ff/

I confront this error:


NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, Dec  4
2017, 14:50:18)
[GCC 5.4.0 20160609]

NOTE2: Please be sure to use the same version of CGenFF in your simulations
that was used during parameter generation:
Traceback (most recent call last):
  File "cgenff_charmm2gmx.py", line 777, in 
check_versions(rtp_name,ffdir + "/forcefield.doc")
  File "cgenff_charmm2gmx.py", line 53, in check_versions
f = open(str_filename, 'r')
IOError: [Errno 2] No such file or directory: 'LIG1.str'

I installed python 2.7.3 for ubuntu, but it seems that it has not been
installed.
please let me know how to solve this error

Thanks a lot
--




*Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics
(IBB)University of Tehran, Tehran- Iran.*
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[gmx-users] cgenff charm error

[marzieh dehghan]

Hi
Dear all
I used charm36 and cgenff (http://mackerell.umaryland.edu/charmm_ff.shtml)
to convert str format of ligand to itp format. when I used the following
command:

python cgenff_charmm2gmx.py LIG lig.mol2 lig.str charmm36-jul2017.ff/

I confront this error:


NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, Dec  4
2017, 14:50:18)
[GCC 5.4.0 20160609]

NOTE2: Please be sure to use the same version of CGenFF in your simulations
that was used during parameter generation:
Traceback (most recent call last):
  File "cgenff_charmm2gmx.py", line 777, in 
check_versions(rtp_name,ffdir + "/forcefield.doc")
  File "cgenff_charmm2gmx.py", line 53, in check_versions
f = open(str_filename, 'r')
IOError: [Errno 2] No such file or directory: 'LIG1.str'

I installed python 2.7.3 for ubuntu, but it seems that it has not been
installed.
please let me know how to solve this error

Thanks a lot
-- 




*Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics
(IBB)University of Tehran, Tehran- Iran.*
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Re: [gmx-users] lie calculations

[Vytautas Rakeviius]

 Hi I think you should check this paper:Åqvist J, Medina C, Samuelsson JE. A 
new method for predicting binding affinity in computer-aided drug design. 
Protein Engineering, Design and Selection. 1994 Mar 1;7(3):385-91.It explains 
everything and gives example of use.And yes with different water models you 
should expect more or less different results.
Also as you see those fitting coefficients in paper like 0.5 or alpha or beta 
etc. I suggest refitting with your own data-set water model force field etc. as 
those numbers depend on such things. That became clear far later after this 
original paper.
On Wednesday, September 12, 2018, 6:35:23 PM GMT+3, Graham Jackson 
 wrote:  
 
 Hi All
I have looked at the manual and can execute LIE but I want to understand the 
process.  The manual gives instructions but no background theory. The theory I 
have seen does not explain how GROMACS does the calculation.  I have a 
simulation of a ligand bound to a receptor embedded in a POPC membrane.  I also 
have a simulation of the ligand in water.  I use these two for the lie 
calculation.  Is this correct and does the choice of water (spc TIP3P Tip4P) 
matter?

Thanks
Graham



—
Professor Graham E Jackson
Department of Chemistry
University of Cape Town
South Africa
+27 21 650 2531

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