Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

[Justin A. Lemkul]

Yun Shi wrote:

Thanks again.

Since I am running MD simulation on a public cluster, I cannot modify 
atomtypes.atp and ffnonbonded.itp on that cluster.




You can make local copies in your working directory and call that force field 
when running grompp.


But I could get every parameter ready and prepare the xxx.tpr files 
locally, and pass them to the cluster. So the practical question is, 
does the tpr file contain all those C12 and C6 LJ parameters already? Or 
mdrun need to retrieve these parameters according to the atom types from 
corresponding files within the gromos53a6.ff folder?




All the necessary information is contained in the .tpr file.

-Justin


Regards,

Yun Shi


Yun Shi wrote:
 > Hi Justin,
 >
 > Thanks a lot for the replies.
 >
 > I wonder what are the "newer versions" you indicated, but I find one as:
 >
 >
 >   /A reoptimized GROMOS force field for hexopyranose-based carbohydrates
 >   accounting for the relative free energies of ring conformers, anomers,
 >   epimers, hydroxymethyl rotamers, and glycosidic linkage conformers/
 >
 > . This new version 56A_CARBO   is claimed to be "nearly equivalent to
 > 53A6 for non-carbohydrate systems", and I find, at least, atomic charges
 > for C1 and C5 look more chemically reasonable.
 >
 > But changes for a couple of 1-4 van der Waals parameter C12 were made to
 > 53a6 force field, and additional atom types were added. So could you
 > tell me which file contain those LJ parameters with respect to different
 > atom types?
 >

New atom types need to be added to atomtypes.atp and their parameters 
defined in

ffnonbonded.itp.

 > Alternatively, would it be reasonably good enough to use your
 > Lysozyme-JZ4 strategy, i.e., to build initial topology of carbohydrate
 > molecules by PRODRG, and then modify the atomic charges according to the
 > 56A_CARBO paper?
 >

Maybe, but check the bonded parameters carefully.  Sugars are particularly
sensitive to incorrect angle and dihedral parameters, especially.

-Justin

--
==
==

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080 


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

[Yun Shi]

Thanks again.

Since I am running MD simulation on a public cluster, I cannot modify
atomtypes.atp and ffnonbonded.itp on that cluster.

But I could get every parameter ready and prepare the xxx.tpr files locally,
and pass them to the cluster. So the practical question is, does the tpr
file contain all those C12 and C6 LJ parameters already? Or mdrun need to
retrieve these parameters according to the atom types from corresponding
files within the gromos53a6.ff folder?

Regards,

Yun Shi


Yun Shi wrote:
> Hi Justin,
>
> Thanks a lot for the replies.
>
> I wonder what are the "newer versions" you indicated, but I find one as:
>
>
>   /A reoptimized GROMOS force field for hexopyranose-based carbohydrates
>   accounting for the relative free energies of ring conformers, anomers,
>   epimers, hydroxymethyl rotamers, and glycosidic linkage conformers/
>
> . This new version 56A_CARBO   is claimed to be "nearly equivalent to
> 53A6 for non-carbohydrate systems", and I find, at least, atomic charges
> for C1 and C5 look more chemically reasonable.
>
> But changes for a couple of 1-4 van der Waals parameter C12 were made to
> 53a6 force field, and additional atom types were added. So could you
> tell me which file contain those LJ parameters with respect to different
> atom types?
>

New atom types need to be added to atomtypes.atp and their parameters
defined in
ffnonbonded.itp.

> Alternatively, would it be reasonably good enough to use your
> Lysozyme-JZ4 strategy, i.e., to build initial topology of carbohydrate
> molecules by PRODRG, and then modify the atomic charges according to the
> 56A_CARBO paper?
>

Maybe, but check the bonded parameters carefully.  Sugars are particularly
sensitive to incorrect angle and dihedral parameters, especially.

-Justin

--
==
==

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

[Justin A. Lemkul]

Yun Shi wrote:

Hi Justin,

Thanks a lot for the replies.

I wonder what are the "newer versions" you indicated, but I find one as:


  /A reoptimized GROMOS force field for hexopyranose-based carbohydrates
  accounting for the relative free energies of ring conformers, anomers,
  epimers, hydroxymethyl rotamers, and glycosidic linkage conformers/

. This new version 56A_CARBO   is claimed to be "nearly equivalent to 
53A6 for non-carbohydrate systems", and I find, at least, atomic charges 
for C1 and C5 look more chemically reasonable.


But changes for a couple of 1-4 van der Waals parameter C12 were made to 
53a6 force field, and additional atom types were added. So could you 
tell me which file contain those LJ parameters with respect to different 
atom types?




New atom types need to be added to atomtypes.atp and their parameters defined in 
ffnonbonded.itp.


Alternatively, would it be reasonably good enough to use your 
Lysozyme-JZ4 strategy, i.e., to build initial topology of carbohydrate 
molecules by PRODRG, and then modify the atomic charges according to the 
56A_CARBO paper?




Maybe, but check the bonded parameters carefully.  Sugars are particularly 
sensitive to incorrect angle and dihedral parameters, especially.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

[Yun Shi]

Hi Justin,

Thanks a lot for the replies.

I wonder what are the "newer versions" you indicated, but I find one as:
*A reoptimized GROMOS force field for hexopyranose-based carbohydrates
accounting for the relative free energies of ring conformers, anomers,
epimers, hydroxymethyl rotamers, and glycosidic linkage conformers*. This
new version 56ACARBO  is claimed to be "nearly equivalent to 53A6 for
non-carbohydrate systems", and I find, at least, atomic charges for C1 and
C5 look more chemically reasonable.

But changes for a couple of 1-4 van der Waals parameter C12 were made to
53a6 force field, and additional atom types were added. So could you tell me
which file contain those LJ parameters with respect to different atom types?

Alternatively, would it be reasonably good enough to use your Lysozyme-JZ4
strategy, i.e., to build initial topology of carbohydrate molecules by
PRODRG, and then modify the atomic charges according to the 56ACARBO paper?

Thanks,

Yun Shi



Yun Shi wrote:
> Hi all,
>
> I am doing MD simulation of some carbohydrate-protein complex with this
> 53a6 force-field.
>
> I noted that in any oligosaccharide, the charge assigned for anomeric
> carbon is 0.232 while C5 (i.e. in a non-terminal mannopyranose) is
> 0.376. This is kind of counter-intuitive for me since the anomeric
> carbon C1 is linked to two oxygen atoms O5 and "O1" while C5 is linked
> to only one oxygen atom O5, and both C1 and C5 are CH type atom. And in
> other force filed like GLYCAM06, C1 always has a larger positive partial
> charge than C5.
>
> I understand that GROMOS force fields are derived in quite different
> ways, but I still wonder if it makes sense to switch the charges on C1
> and C5?
>

No, but the charges used may not be the best ones anyway.  There are newer
revisions of 53A6 that are much better.

> It seems these carbohydrate parameters did not change in the new 54a7
> ff, which was tested against nOe and J-coupling data rather than free
> enthalpy of hydration and solvation, which really puzzles me.
>

54A7 was principally a revision of protein atom types and one lipid type;
nothing in the sugar parameters was modified.

-Justin

--
==
==

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

[Justin A. Lemkul]

Yun Shi wrote:

Hi all,

I am doing MD simulation of some carbohydrate-protein complex with this 
53a6 force-field.


I noted that in any oligosaccharide, the charge assigned for anomeric 
carbon is 0.232 while C5 (i.e. in a non-terminal mannopyranose) is 
0.376. This is kind of counter-intuitive for me since the anomeric 
carbon C1 is linked to two oxygen atoms O5 and "O1" while C5 is linked 
to only one oxygen atom O5, and both C1 and C5 are CH type atom. And in 
other force filed like GLYCAM06, C1 always has a larger positive partial 
charge than C5.


I understand that GROMOS force fields are derived in quite different 
ways, but I still wonder if it makes sense to switch the charges on C1 
and C5?




No, but the charges used may not be the best ones anyway.  There are newer 
revisions of 53A6 that are much better.


It seems these carbohydrate parameters did not change in the new 54a7 
ff, which was tested against nOe and J-coupling data rather than free 
enthalpy of hydration and solvation, which really puzzles me.




54A7 was principally a revision of protein atom types and one lipid type; 
nothing in the sugar parameters was modified.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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