Re: [gmx-users] converting parmbsc0 dihedrals to RB function

[gportel]

Hi,

Right, the only dihedral angles that do not allow an exact translation to
RB because of the phase are the ones involving the new parametrization for
nucleic acids. Namely, it corrects the alpha/gamma transitions to get the
populations of states right, thus avoiding the loss of helicity on the
long run. For proteins, there's no difference at all, so you can use
ffamber.

I've used the combined approach you mention without problems. The only
thing is that I do not use pdb2gmx. Rather I use amber's tools
(leap+libraries, all free in ambertools) to get a topology, and then I use
a slightly modified version of amb2gmx.pl script to get a gromacs
topology. I only convert the new parmbsc0 dihedrals to type 1 if the phase
does not allow a direct conversion to RB form. Typically you have three
entries for the same dihedral, this is no problem at the itp level, grompp
captures them all. With this approach I reproduced a torsional scan of
parmbsc0 from amber md tool using gromacs, so I feel confident about it.

Another option is to use the ffamber parameters and change the itp file
including the new ones.

I should also mention that I had problems importing the new dihedrals
using pdb2gmx. IIRC, pdb2gmx will only use one definition for dihedral if
type 1 or 3 is used. There was a new dihedral type that could be used in
the development versions, but... for a reason it did not work out for me,
don't recall exactly why. It could well be that it would have worked with
more patience from my side.

Hope this helped, somehow. You were on the right direction anyway.

best,

Guillem


Mark Abraham wrote:
> On 8/04/2010 10:32 PM, Vigneshwar Ramakrishnan wrote:
>> Dear Dr. Mark,
>>
>> Thanks very much for pointing out that GROMACS can handle multiple
>> instances of the parameters with different n for a single dihedral.
>
> I hope I'm right there. There's been discussion on such topics before.
There's some subtle difference between [ dihedrals ] and [ dihedraltypes
] which eludes my memory, but which will be in the archives.
>
>> However, given that, in the existing ffamber ports in GROMACS  the other
>> dihedral parameters have been converted to RB form, would it make a
>> difference to just import these new parameters in the non-RB form?
>
> It will make no numerical difference, but g_energy will probably report
the contribution from the two different functional forms separately.
Attempting to mix *non-bonded* interactions in this kind of way asks for
trouble, because the maths is not well-defined. Here, you're fine,
because the maths is right.
>
>> To my knowledge, the torsional term should not vary (or, vary within
>> acceptable limits) irrespective of the functional form used to calculate
>> it. But I would like to know if there could be some reason for which
>> this assumption cannot be made.
>
> The R-B form might be more efficient to evaluate than a sum of simple
dihedrals in the cases where the angle is zero or 180, which might
explain the ffamber practice.
>
> Mark
>
>> Dear Dr. Alan,
>>
>> Thanks very much for pointing out to the acpypi code. I was able to
>> better understand the conversion procedure.
>>
>> Sincerely,
>> Vignesh
>>
>> On Wed, Apr 7, 2010 at 10:04 PM, Mark Abraham > > wrote:
>>
>> On 7/04/2010 7:44 PM, Vigneshwar Ramakrishnan wrote:
>>
>> Dear Users,
>>
>> I am trying to port the new parmbsc0 forcefield
>> (http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs
for DNA
>> simulations.
>>
>> While unit conversions are sufficient to convert many of the
>> parameters
>> from AMBER to GROMACS format, dihedral angle conversion does not
>> seem to
>> be straight forward - the dihedral parameters need to be
>> converted to
>> the Ryckaert-Bellemans parameters.
>>
>>
>> Why? GROMACS can probably do the non-RB form - IIRC you can
>> implement a sum of multiple instances of 4.61 with different n.
>>
>>
>> I went through the GROMACS 4.0
>> manual, especially equations 4.61-4.65 to understand the
>> procedure. The
>> procedure involves comparing the fourier expansion of the IUPAC
>> convention of dihedral potential (equation 4.65) with the
>> Ryckaert-Bellemans (RB) functional of dihedral potential
>> (equation 4.62)
>> to get the Cn's of the RB function. However, I am not able to
>> understand
>> how to account for the phase angles. (Also to note, the parmbsc0
>> forcefield contains phase angles other than 0 and 180.)
>>
>>
>> Elegant conversion formulae require those angles to be convenient...
>>
>> Mark
>>
>>
>>   Any advice or suggestion will be of great help.
>>
>> Thank you,
>>



Dr. Guillem Portella
- MMB - Institute for Research in Biomedicine
- Parc Cientific de Barcelona -
http://mmb.pcb.ub.es/~gportella



-- 
gmx-users mailing listgmx-users@grom

Re: [gmx-users] converting parmbsc0 dihedrals to RB function

[Mark Abraham]

On 8/04/2010 10:32 PM, Vigneshwar Ramakrishnan wrote:

Dear Dr. Mark,

Thanks very much for pointing out that GROMACS can handle multiple
instances of the parameters with different n for a single dihedral.


I hope I'm right there. There's been discussion on such topics before. 
There's some subtle difference between [ dihedrals ] and [ dihedraltypes 
] which eludes my memory, but which will be in the archives.



However, given that, in the existing ffamber ports in GROMACS  the other
dihedral parameters have been converted to RB form, would it make a
difference to just import these new parameters in the non-RB form?


It will make no numerical difference, but g_energy will probably report 
the contribution from the two different functional forms separately. 
Attempting to mix *non-bonded* interactions in this kind of way asks for 
trouble, because the maths is not well-defined. Here, you're fine, 
because the maths is right.



To my knowledge, the torsional term should not vary (or, vary within
acceptable limits) irrespective of the functional form used to calculate
it. But I would like to know if there could be some reason for which
this assumption cannot be made.


The R-B form might be more efficient to evaluate than a sum of simple 
dihedrals in the cases where the angle is zero or 180, which might 
explain the ffamber practice.


Mark


Dear Dr. Alan,

Thanks very much for pointing out to the acpypi code. I was able to
better understand the conversion procedure.

Sincerely,
Vignesh

On Wed, Apr 7, 2010 at 10:04 PM, Mark Abraham mailto:mark.abra...@anu.edu.au>> wrote:

On 7/04/2010 7:44 PM, Vigneshwar Ramakrishnan wrote:

Dear Users,

I am trying to port the new parmbsc0 forcefield
(http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA
simulations.

While unit conversions are sufficient to convert many of the
parameters
from AMBER to GROMACS format, dihedral angle conversion does not
seem to
be straight forward - the dihedral parameters need to be
converted to
the Ryckaert-Bellemans parameters.


Why? GROMACS can probably do the non-RB form - IIRC you can
implement a sum of multiple instances of 4.61 with different n.


I went through the GROMACS 4.0
manual, especially equations 4.61-4.65 to understand the
procedure. The
procedure involves comparing the fourier expansion of the IUPAC
convention of dihedral potential (equation 4.65) with the
Ryckaert-Bellemans (RB) functional of dihedral potential
(equation 4.62)
to get the Cn's of the RB function. However, I am not able to
understand
how to account for the phase angles. (Also to note, the parmbsc0
forcefield contains phase angles other than 0 and 180.)


Elegant conversion formulae require those angles to be convenient...

Mark


  Any advice or suggestion will be of great help.

Thank you,

Vignesh

--
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

I arise in the morning torn between a desire to improve the
world and a
desire to enjoy the world. This makes it hard to plan the day.
(E.B. White)

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--
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

I arise in the morning torn between a desire to improve the world and a
desire to enjoy the world. This makes it hard to plan the day. (E.B. White)


--
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Re: [gmx-users] converting parmbsc0 dihedrals to RB function

[Vigneshwar Ramakrishnan]

Dear Dr. Mark,

Thanks very much for pointing out that GROMACS can handle multiple instances
of the parameters with different n for a single dihedral.

However, given that, in the existing ffamber ports in GROMACS  the other
dihedral parameters have been converted to RB form, would it make a
difference to just import these new parameters in the non-RB form?

To my knowledge, the torsional term should not vary (or, vary within
acceptable limits) irrespective of the functional form used to calculate it.
But I would like to know if there could be some reason for which this
assumption cannot be made.

Dear Dr. Alan,

Thanks very much for pointing out to the acpypi code. I was able to better
understand the conversion procedure.

Sincerely,
Vignesh

On Wed, Apr 7, 2010 at 10:04 PM, Mark Abraham wrote:

> On 7/04/2010 7:44 PM, Vigneshwar Ramakrishnan wrote:
>
>> Dear Users,
>>
>> I am trying to port the new parmbsc0 forcefield
>> (http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA
>> simulations.
>>
>> While unit conversions are sufficient to convert many of the parameters
>> from AMBER to GROMACS format, dihedral angle conversion does not seem to
>> be straight forward - the dihedral parameters need to be converted to
>> the Ryckaert-Bellemans parameters.
>>
>
> Why? GROMACS can probably do the non-RB form - IIRC you can implement a sum
> of multiple instances of 4.61 with different n.
>
>
>  I went through the GROMACS 4.0
>> manual, especially equations 4.61-4.65 to understand the procedure. The
>> procedure involves comparing the fourier expansion of the IUPAC
>> convention of dihedral potential (equation 4.65) with the
>> Ryckaert-Bellemans (RB) functional of dihedral potential (equation 4.62)
>> to get the Cn's of the RB function. However, I am not able to understand
>> how to account for the phase angles. (Also to note, the parmbsc0
>> forcefield contains phase angles other than 0 and 180.)
>>
>
> Elegant conversion formulae require those angles to be convenient...
>
> Mark
>
>
>   Any advice or suggestion will be of great help.
>>
>> Thank you,
>>
>> Vignesh
>>
>> --
>> R.Vigneshwar
>> Graduate Student,
>> Dept. of Chemical & Biomolecular Engg,
>> National University of Singapore,
>> Singapore
>>
>> "Strive for Excellence, Never be satisfied with the second Best!!"
>>
>> I arise in the morning torn between a desire to improve the world and a
>> desire to enjoy the world. This makes it hard to plan the day. (E.B.
>> White)
>>
>>  --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

I arise in the morning torn between a desire to improve the world and a
desire to enjoy the world. This makes it hard to plan the day. (E.B. White)
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] converting parmbsc0 dihedrals to RB function

[Mark Abraham]

On 7/04/2010 7:44 PM, Vigneshwar Ramakrishnan wrote:

Dear Users,

I am trying to port the new parmbsc0 forcefield
(http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA
simulations.

While unit conversions are sufficient to convert many of the parameters
from AMBER to GROMACS format, dihedral angle conversion does not seem to
be straight forward - the dihedral parameters need to be converted to
the Ryckaert-Bellemans parameters.


Why? GROMACS can probably do the non-RB form - IIRC you can implement a 
sum of multiple instances of 4.61 with different n.



I went through the GROMACS 4.0
manual, especially equations 4.61-4.65 to understand the procedure. The
procedure involves comparing the fourier expansion of the IUPAC
convention of dihedral potential (equation 4.65) with the
Ryckaert-Bellemans (RB) functional of dihedral potential (equation 4.62)
to get the Cn's of the RB function. However, I am not able to understand
how to account for the phase angles. (Also to note, the parmbsc0
forcefield contains phase angles other than 0 and 180.)


Elegant conversion formulae require those angles to be convenient...

Mark


  Any advice or suggestion will be of great help.

Thank you,

Vignesh

--
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

I arise in the morning torn between a desire to improve the world and a
desire to enjoy the world. This makes it hard to plan the day. (E.B. White)


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] converting parmbsc0 dihedrals to RB function

[Vigneshwar Ramakrishnan]

Dear Users,



I am trying to port the new parmbsc0 forcefield (
http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA
simulations.

While unit conversions are sufficient to convert many of the parameters from
AMBER to GROMACS format, dihedral angle conversion does not seem to be
straight forward - the dihedral parameters need to be converted to the
Ryckaert-Bellemans parameters. I went through the GROMACS 4.0 manual,
especially equations 4.61-4.65 to understand the procedure. The procedure
involves comparing the fourier expansion of the IUPAC convention of dihedral
potential (equation 4.65) with the Ryckaert-Bellemans (RB) functional of
dihedral potential (equation 4.62) to get the Cn's of the RB function.
However, I am not able to understand how to account for the phase angles.
(Also to note, the parmbsc0 forcefield contains phase angles other than 0
and 180.)



 Any advice or suggestion will be of great help.



Thank you,

Vignesh

-- 
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

I arise in the morning torn between a desire to improve the world and a
desire to enjoy the world. This makes it hard to plan the day. (E.B. White)
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php