Re: [gmx-users] Conversion Amber to Gromacs

2017-10-24 Thread Alan 
Please, get it here

svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
stable/ccpn/python/acpype acpype

Interestingly, but Google code still holds the correct information too:

https://code.google.com/archive/p/acpype/


On 24 October 2017 at 18:34, ABEL Stephane <stephane.a...@cea.fr> wrote:

> Hello Elisa,
>
> "J'arrive après la bataille" To be sure that you have correct Amber
> parameters for GROMACS, you could also use the acpype suite*. This suite
> converts  Amber params in gromacs format. The program generates the
> (non)ffbonded.itp and top files in gromacs format from the Amber's LeaP
> tool. It also provides some gromacs and Amber files to perform and a single
> point energy to test if the conversion is correctly done.
>
> I used successfully this code  to convert the Amber lipid14 params for
> POPC lipid in the GROMACS format.
>
> *http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder
>
> HTH
>
> Stéphane
>
> --
>
> Message: 3
> Date: Tue, 24 Oct 2017 17:17:08 +0200
> From: Elisa Pieri <elisa.pi...@univ-amu.fr>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Conversion Amber to Gromacs
> Message-ID:
>

[gmx-users] Conversion Amber to Gromacs

2017-10-24 Thread ABEL Stephane 
Hello Elisa, 

"J'arrive après la bataille" To be sure that you have correct Amber parameters 
for GROMACS, you could also use the acpype suite*. This suite converts  Amber 
params in gromacs format. The program generates the (non)ffbonded.itp and top 
files in gromacs format from the Amber's LeaP tool. It also provides some 
gromacs and Amber files to perform and a single point energy to test if the 
conversion is correctly done. 

I used successfully this code  to convert the Amber lipid14 params for POPC 
lipid in the GROMACS format.

*http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder

HTH 

Stéphane  

--

Message: 3
Date: Tue, 24 Oct 2017 17:17:08 +0200
From: Elisa Pieri <elisa.pi...@univ-amu.fr>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Conversion Amber to Gromacs
Message-ID:

Re: [gmx-users] Conversion Amber to Gromacs

2017-10-23 Thread Mark Abraham 
On Mon, Oct 23, 2017 at 11:10 AM Elisa Pieri 
wrote:

> Hello again,
>
> sorry I wasn't very clear perhaps..we are trying to modify directly the
> ffbonded.itp file (together with all the other interested ones) in the
> Amber94 force field in order to include the Amber Lipids17 force field. We
> added most of the parameters with no problems (bond equilibrium lengths,
> constants, bending and so on), but we were not able to understand what is
> the conversion factor for torsion parameters between the Amber software
> Suite and Gromacs. I know that in the Amber package, the dihedral force
> constant is expressed in Kcal/mol, but I couldn't understand what are the
> units (and therefore how to convert the parameters) in Gromacs.
>

Chapter 2 of the reference manual describes the units. Chapter 4 describes
the functional forms, and e.g. tables in chapter 5 fill in the gaps. That
has always been enough for me when converting stuff to and from AMBER
descriptions.

Mark


> Any idea?
> Elisa
>
> On Fri, Oct 20, 2017 at 7:17 PM, p.kartheek 
> wrote:
>
> > ParmEd (https://parmed.github.io/ParmEd/html/parmed.html) would be the
> > appropriate software for converting topologies.
> > This is the parm.py  script I have employed, supply amber topologies
> > file.prmtop and file.inpcrd as input and amber.save option will give
> > converted gromacs topologies as output.
> >
> > import parmed as pmd
> > #amber = pmd.load_file('prmtop', 'inpcrd')
> > amber = pmd.load_file('new24_ang.prmtop', 'new24_ang.inpcrd')
> > #save a GROMACS topology and GRO file
> > amber.save('new24_ang.top')
> > amber.save('new24_ang.gro')
> >
> >
> > --
> > P. Kartheek,
> > PhD Candidate, Computational Biophysical Chemistry,
> > Center for Computational Natural Sciences and Bioinformatics,
> > International Institute of Information Technology,
> > Marimuthu Krishan Group,
> > 9701577399,
> > karthee...@research.iiit.ac.in,
> >
> >
> > On Fri, Oct 20, 2017 at 10:30 PM, p.kartheek 
> > wrote:
> >
> > > You can do with ParmEd
> > > On Oct 20, 2017 10:07 PM, "Elisa Pieri" 
> wrote:
> > >
> > >> Hello GMX users/developers,
> > >>
> > >> we are trying to add the Amber lipids17 forcefield to the Amber99
> > >> forcefield implemented in Gromacs. We are a little bit lost on the
> > torsion
> > >> parameters: how to convert the constant from Amber to Gromacs?
> > >>
> > >> Thank you in advance!
> > >> Elisa
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at http://www.gromacs.org/Support
> > >> /Mailing_Lists/GMX-Users_List before posting!
> > >>
> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>
> > >> * For (un)subscribe requests visit
> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > >> send a mail to gmx-users-requ...@gromacs.org.
> > >>
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

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

Re: [gmx-users] Conversion Amber to Gromacs

2017-10-23 Thread Thomas Piggot 

Hi,

The multiplicity/periodicity is the same but always positive in GROMACS. 
Kd in GROMACS is the AMBER value multiplied by 4.184 then divided by 
IDIVF (the entry after names in AMBER file). The phase is the same.


For more info on why see ambermd.org/formats.html#parm.dat

Cheers

Tom

On 23/10/17 10:09, Elisa Pieri wrote:

Hello again,

sorry I wasn't very clear perhaps..we are trying to modify directly the
ffbonded.itp file (together with all the other interested ones) in the
Amber94 force field in order to include the Amber Lipids17 force field. We
added most of the parameters with no problems (bond equilibrium lengths,
constants, bending and so on), but we were not able to understand what is
the conversion factor for torsion parameters between the Amber software
Suite and Gromacs. I know that in the Amber package, the dihedral force
constant is expressed in Kcal/mol, but I couldn't understand what are the
units (and therefore how to convert the parameters) in Gromacs.

Any idea?
Elisa

On Fri, Oct 20, 2017 at 7:17 PM, p.kartheek  wrote:


ParmEd (https://parmed.github.io/ParmEd/html/parmed.html) would be the
appropriate software for converting topologies.
This is the parm.py  script I have employed, supply amber topologies
file.prmtop and file.inpcrd as input and amber.save option will give
converted gromacs topologies as output.

import parmed as pmd
#amber = pmd.load_file('prmtop', 'inpcrd')
amber = pmd.load_file('new24_ang.prmtop', 'new24_ang.inpcrd')
#save a GROMACS topology and GRO file
amber.save('new24_ang.top')
amber.save('new24_ang.gro')


--
P. Kartheek,
PhD Candidate, Computational Biophysical Chemistry,
Center for Computational Natural Sciences and Bioinformatics,
International Institute of Information Technology,
Marimuthu Krishan Group,
9701577399,
karthee...@research.iiit.ac.in,


On Fri, Oct 20, 2017 at 10:30 PM, p.kartheek 
wrote:


You can do with ParmEd
On Oct 20, 2017 10:07 PM, "Elisa Pieri"  wrote:


Hello GMX users/developers,

we are trying to add the Amber lipids17 forcefield to the Amber99
forcefield implemented in Gromacs. We are a little bit lost on the

torsion

parameters: how to convert the constant from Amber to Gromacs?

Thank you in advance!
Elisa
--
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.



--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.

--
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] Conversion Amber to Gromacs

2017-10-23 Thread Elisa Pieri 
Hello again,

sorry I wasn't very clear perhaps..we are trying to modify directly the
ffbonded.itp file (together with all the other interested ones) in the
Amber94 force field in order to include the Amber Lipids17 force field. We
added most of the parameters with no problems (bond equilibrium lengths,
constants, bending and so on), but we were not able to understand what is
the conversion factor for torsion parameters between the Amber software
Suite and Gromacs. I know that in the Amber package, the dihedral force
constant is expressed in Kcal/mol, but I couldn't understand what are the
units (and therefore how to convert the parameters) in Gromacs.

Any idea?
Elisa

On Fri, Oct 20, 2017 at 7:17 PM, p.kartheek  wrote:

> ParmEd (https://parmed.github.io/ParmEd/html/parmed.html) would be the
> appropriate software for converting topologies.
> This is the parm.py  script I have employed, supply amber topologies
> file.prmtop and file.inpcrd as input and amber.save option will give
> converted gromacs topologies as output.
>
> import parmed as pmd
> #amber = pmd.load_file('prmtop', 'inpcrd')
> amber = pmd.load_file('new24_ang.prmtop', 'new24_ang.inpcrd')
> #save a GROMACS topology and GRO file
> amber.save('new24_ang.top')
> amber.save('new24_ang.gro')
>
>
> --
> P. Kartheek,
> PhD Candidate, Computational Biophysical Chemistry,
> Center for Computational Natural Sciences and Bioinformatics,
> International Institute of Information Technology,
> Marimuthu Krishan Group,
> 9701577399,
> karthee...@research.iiit.ac.in,
>
>
> On Fri, Oct 20, 2017 at 10:30 PM, p.kartheek 
> wrote:
>
> > You can do with ParmEd
> > On Oct 20, 2017 10:07 PM, "Elisa Pieri"  wrote:
> >
> >> Hello GMX users/developers,
> >>
> >> we are trying to add the Amber lipids17 forcefield to the Amber99
> >> forcefield implemented in Gromacs. We are a little bit lost on the
> torsion
> >> parameters: how to convert the constant from Amber to Gromacs?
> >>
> >> Thank you in advance!
> >> Elisa
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/Support
> >> /Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

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

Re: [gmx-users] Conversion Amber to Gromacs

2017-10-20 Thread p.kartheek 
ParmEd (https://parmed.github.io/ParmEd/html/parmed.html) would be the
appropriate software for converting topologies.
This is the parm.py  script I have employed, supply amber topologies
file.prmtop and file.inpcrd as input and amber.save option will give
converted gromacs topologies as output.

import parmed as pmd
#amber = pmd.load_file('prmtop', 'inpcrd')
amber = pmd.load_file('new24_ang.prmtop', 'new24_ang.inpcrd')
#save a GROMACS topology and GRO file
amber.save('new24_ang.top')
amber.save('new24_ang.gro')


--
P. Kartheek,
PhD Candidate, Computational Biophysical Chemistry,
Center for Computational Natural Sciences and Bioinformatics,
International Institute of Information Technology,
Marimuthu Krishan Group,
9701577399,
karthee...@research.iiit.ac.in,


On Fri, Oct 20, 2017 at 10:30 PM, p.kartheek 
wrote:

> You can do with ParmEd
> On Oct 20, 2017 10:07 PM, "Elisa Pieri"  wrote:
>
>> Hello GMX users/developers,
>>
>> we are trying to add the Amber lipids17 forcefield to the Amber99
>> forcefield implemented in Gromacs. We are a little bit lost on the torsion
>> parameters: how to convert the constant from Amber to Gromacs?
>>
>> Thank you in advance!
>> Elisa
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

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

Re: [gmx-users] Conversion Amber to Gromacs

2017-10-20 Thread p.kartheek 
You can do with ParmEd
On Oct 20, 2017 10:07 PM, "Elisa Pieri"  wrote:

> Hello GMX users/developers,
>
> we are trying to add the Amber lipids17 forcefield to the Amber99
> forcefield implemented in Gromacs. We are a little bit lost on the torsion
> parameters: how to convert the constant from Amber to Gromacs?
>
> Thank you in advance!
> Elisa
> --
> 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.

[gmx-users] Conversion Amber to Gromacs

2017-10-20 Thread Elisa Pieri 
Hello GMX users/developers,

we are trying to add the Amber lipids17 forcefield to the Amber99
forcefield implemented in Gromacs. We are a little bit lost on the torsion
parameters: how to convert the constant from Amber to Gromacs?

Thank you in advance!
Elisa
-- 
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.