[gmx-users] Thesis developed software; which Open-source License?

[Henry Wittler]

Greetings comrades. This question may be somewhat redundant, so dont expect
reply to every aspect, may ask at RG also. However if anyone have more or
less insight, please reply.

My thesis has calculation software that are built upon partly innovative
and partly basic calculation/plotting/graphing software based upon
"VMD/tcl” coding, GROMACS (GMX) and Python/MatplotlibScipy/Numpy (etc).
The solvated protein data (chap. 6 of thesis) are obtained from GMX
simulations, moreover the analysis data by VMD/tcl etc.

I have uploaded so far just part of the code (for chap. 4.1) I intend to
upload code from whole thesis to github link
https://wittler-github.github.io/A_MD_Analysis_of_Insulin/
The following thesis link(downloadable) contains the calculated data along
with the graphs.

http://hdl.handle.net/1959.9/568798  (
https://www.researchgate.net/project/A-Molecular-Dynamics-Analysis-of-Insulin)


I mainly want to share the novel GMX simulated data and tools I’ve
developed from the above-mentioned softwares, that are described in my
thesis. I do not expect to contribute to GMX directly from this repository,
possibly via other created repository if so.

Currently I have applied the BSD-3 clause version, which I understand to be
the most relevant and simple to use. Choice is not set-in stone it appears,
however if changing I understand one need to notify everyone that has taken
part of, or are using the code.
The BSD-3 do appears to be one of the most popular for open-source code and
compatible between different softwares. I thought of using LGPL2 since GMX
uses that, however BSD-3 does appear more simple to understand. The only
innovative scripts including GMX are just linux bash/automatic scripts that
make the simulation of replicas straightforward. Can I share these script
under the BSD-3 license, even though technically they are modified scripts
using standard gmx commands (not altering the original gmx software
v.5.0.4)? Can I share some of the GMX code (parameter files etc) and some
of the original GMX simulated solvated protein data (in addition to data
calculated/graphed by matplotlib etc), at my github repository with no
issues between BSD-3 license and LGPL2?

The other python, and VMD/tcl softwares I do not see any issue with. Are
there any clash with these above-mentioned softwares to be aware of?

Any other insights anyone else has here about open-source licensing when
distributing code?

*Kind regards,*

*Dr. Henry P.A. Wittler*

*Department of Chemistry and Physics, LIMS, La Trobe University,
MelbourneWorking in Ludvika, Sweden*
*Skype: henry.wittler*
Researchgate & Linkedin
linkedin.com/in/henry-per-andreas-wittler-b03256191

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Re: [gmx-users] D- &/or L- cmap for charmm36

[HENRY WITTLER]

Thanks for previous replies Justin.

Since Im at the end of my PhD and the D-aa simulation is just an extra to the 
PhD-project. I can keep the charmm36 D-aa files etc, if I need to continue this 
later,
so I have the old cmap parameters to match my old gmx. 5.0.4. charmm36-mars2014 
L-aa simulation.
Not sure if I can dig deeper to answer my next question, if it is something I 
can solve myself I dont expect a reply.
The CMAP energy unit conversion from CHARMM to GMX, do not seem straightforward 
to me, since the format is different, see below.  Is there a script to do this 
conversion readily?

GMX
; This force field generated by charmm2gmx.py from
; multiple charmm parameter files
; and multiple charmm topology files
[ cmaptypes ]
C NH1 CT1 C NH1 1 24 24\
0.53048936 3.21624080 4.06375184 5.23405848 8.87430584 11.38227912 8.74221696 
7.48848136 3.26716008 -2.88057522\
4.18872792 -9.20697568 -20.19897128 -20.17293425 -20.55692503 -15.02518750 
-11.57481006 -11.64909280 -10.2738 -9.81981034\
-9.77110440 -6.37079270 -3.98125173 -0.15334360 -0.53192447 5.76174456 
6.59825168 7.83366136 10.03737416 10.40405992\
10.19537874 8.07122888 4.54573190 2.69198560 1.08230038 -11.71704096 
-16.77565177 -17.30212030 -14.30965656 -10.88735376\
-9.61955155 -6.28119234 -4.60984752 -3.60423986 -2.67846291 -0.86902098 
-4.50342330 -4.69457352 0.35174470 5.94260633\

CHARMM
CMAP
! 2D grid correction data.
! Finalfix3, Feig/Best/MacKerell 2010

! Jing Huang/Alex MacKerell adjustments to correct for
! oversampling of alpha L conformation.  2016/1

!Direct conversion using Jared Ostmeyer/Benoit Roux flip_cmap.py script
!to invert L CMAP to create D CMAP.  Proline unchanged.

! D-alanine map--
! note the new type for the alpha carbon
CNH1  CTD1  CNH1  CTD1  CNH1   24

! phi = -180.0
 0.13 -0.04 -0.95 -1.52 -2.34
-2.35 -2.45 -2.78 -2.77 -3.59
-4.91 -4.82 -4.83 -2.20  1.00
-0.69  0.78  1.79  2.09  2.72
 2.12  1.25  0.97  0.77

! phi = -165.0
-0.81 -1.81 -2.75 -3.25 -3.55
-3.56 -3.84 -3.67 -4.19 -5.14
-5.89 -6.41 -4.56 -0.74 -2.74
-1.09  0.63  1.52  1.70  1.64
 1.28  0.54  0.38 -0.07

Cheers,
Henry

On 10/4/16 2:00 AM, HENRY WITTLER wrote:
>
> Thanks, for the previous reply.
>
> Will the CHARMM cmap and topology for D-amino acids be included in gmx for a 
> later version of gmx charmm36?

It doesn't seem straightforward to convert the charmm D-aa cmap parameters to 
gmx cmap.itp format.
Can this program be used for this 'cgenff_charmm2gmx.py' at 
http://mackerell.umaryland.edu/charmm_ff.shtml#charmm
>

I will consider putting it in.  Note that we have an update to the CHARMM36
protein parameters (specifically CMAP) that is about to be published, so no
update will be posted until then (though the files, in CHARMM format, are
available, but we're waiting on the conversion until the reference is
available).  The D-amino acid CMAP, however, has not been adjusted, but can
easily be converted.

In the meantime, you can certainly proceed with the existing files.  The CMAP
conversion is just converting energy units.  And a new DSER entry would just
require changing the CA type in the existing SER .rtp entry to create a new 
residue.

-Justin

>
> Cheers,
> Henry Wittler
>
> Phd in Molecular modelling group (Brian J. Smith)
> Department of Chemistry and Physics, La Trobe Institute for Molecular 
> Science, La Trobe University, Victoria 3086, Australia
> Tel: 0432901627
>
>
>
> Message: 3
> Date: Wed, 21 Sep 2016 15:08:23 -0400
> From: Justin Lemkul  vt.edu<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>>
> To: gmx-users at 
> gromacs.org<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
> Subject: Re: [gmx-users] D- &/or L- cmap for charmm36
> Message-ID: <5156078a-2572-401b-ec29-62dd5ae8bb6f at 
> vt.edu<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 9/21/16 1:43 AM, HENRY WITTLER wrote:
>> Greetings.
>>
>>
>> If anyone can give insight please.
>>
>>
>> I want to do a MD for insulin a 51aa protein, mutating one residue from L to 
>> D-Ser.
>>
>> I have runned 1.5us for the L- Ser (with cmap), and want to repeat it for 
>> the D-Ser, with gmx v.5.0.4 charmm36 mars14 version.
>>
>>
>> It seems in the traditional CHARMM one have to change dihedrals involved 
>> with changing L- to D-
(http://www.ks.u

Re: [gmx-users] D- &/or L- cmap for charmm36 (gromacs.org_gmx-users Digest, Vol 149, Issue 71)

[HENRY WITTLER]

Thanks, for the previous reply.

Will the CHARMM cmap and topology for D-amino acids be included in gmx for a 
later version of gmx charmm36? It doesn't seem straightforward to convert the 
charmm D-aa cmap parameters to gmx cmap.itp format. Can this program be used 
for this 'cgenff_charmm2gmx.py' at 
http://mackerell.umaryland.edu/charmm_ff.shtml#charmm


Cheers,
Henry Wittler

Phd in Molecular modelling group (Brian J. Smith)
Department of Chemistry and Physics, La Trobe Institute for Molecular Science, 
La Trobe University, Victoria 3086, Australia
Tel: 0432901627



Message: 3
Date: Wed, 21 Sep 2016 15:08:23 -0400
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] D- &/or L- cmap for charmm36
Message-ID: <5156078a-2572-401b-ec29-62dd5ae8b...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed



On 9/21/16 1:43 AM, HENRY WITTLER wrote:
> Greetings.
>
>
> If anyone can give insight please.
>
>
> I want to do a MD for insulin a 51aa protein, mutating one residue from L to 
> D-Ser.
>
> I have runned 1.5us for the L- Ser (with cmap), and want to repeat it for the 
> D-Ser, with gmx v.5.0.4 charmm36 mars14 version.
>
>
> It seems in the traditional CHARMM one have to change dihedrals involved with 
> changing L- to D- 
> (http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/node4.html),
>  also the cmap is for L-aa 
> (http://mackerell.umaryland.edu/~kenno/cgenff/faq.php<http://mackerell.umaryland.edu/%7Ekenno/cgenff/faq.php>).
>
>
> In link http://www.swisssidechain.ch/D_residues.php gives topology D-aa for 
> gmx-charmm, without changing anything about cmap.itp, only .hdb and .rtp.
>
>
> Previous discussions 
> (http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/r1t0ZqeF/converting-l-to-d-amino-acid-in-the-charmm-force-field-in-gromacs-where-to-alter-dihedral)
>  and my own testing MD and looking at it in vmd etc, seems to imply that the 
> .top, .itp do not distinguish about chirality, is this the case?
>
> How is cmap.itp implemented in gmx, is these parameters for L-, and D- 
> aminoacids?
>

The parameters provided are for L-amino acids.  There are D-amino acid CMAP
parameters available in CHARMM, but not in GROMACS format.  See the latest force
field distribution on http://mackerell.umaryland.edu/charmm_ff.shtml#charmm and
look in stream/prot/toppar_all36_prot_d_aminoacids.str

The D vs L stereochemistry is made possible by assigning a special atom type to
the CA atom (CTD1 instead of CT1) so you can apply residue-specific parameters.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul<http://mackerell.umaryland.edu/%7Ejalemkul>

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[gmx-users] D- &/or L- cmap for charmm36

[HENRY WITTLER]

Greetings.


If anyone can give insight please.


I want to do a MD for insulin a 51aa protein, mutating one residue from L to 
D-Ser.

I have runned 1.5us for the L- Ser (with cmap), and want to repeat it for the 
D-Ser, with gmx v.5.0.4 charmm36 mars14 version.


It seems in the traditional CHARMM one have to change dihedrals involved with 
changing L- to D- 
(http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/node4.html),
 also the cmap is for L-aa 
(http://mackerell.umaryland.edu/~kenno/cgenff/faq.php).


In link http://www.swisssidechain.ch/D_residues.php gives topology D-aa for 
gmx-charmm, without changing anything about cmap.itp, only .hdb and .rtp.


Previous discussions 
(http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/r1t0ZqeF/converting-l-to-d-amino-acid-in-the-charmm-force-field-in-gromacs-where-to-alter-dihedral)
 and my own testing MD and looking at it in vmd etc, seems to imply that the 
.top, .itp do not distinguish about chirality, is this the case?

How is cmap.itp implemented in gmx, is these parameters for L-, and D- 
aminoacids?


Cheers,

Henry Wittler

Phd in Molecular modelling group (Brian J. Smith)
Department of Chemistry and Physics, La Trobe Institute for Molecular Science, 
La Trobe University, Victoria 3086, Australia

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