[gmx-users] problem with simulation of phosphatidic acid, possibly in my topology?

[Yiannis]

Dear Maria,
I am not sure but something you should look further is the rotation  
around your P3-O2 bond (which is P8-O7 in Tieleman's topology).
It is described by the first two lines of your dihedral section  
topology:
    1     2     3     6     1    0.0     1.05   3
    1     2     3     6     1    0.0     3.14   2
which I see you took identical to the corresponding lines of Tieleman.

But in your case this is a rotation around O-P-O-H and in POPC it's  
around O-P-O-C

I would expect that the function fitting these two dihedrals changes  
between POPC and POPA.

Probably the P-O-H angle should also differ from the P-O-C and that  
could have an influence on the other angles around P.

These two parts of the topology are I believe to be verified.

Ioannis


Le 5 mai 08 à 15:53, maria goranovic a écrit :

> Dear Mark,
>
> Sorry, perhaps I should have clarified more. I did not just make a  
> blind substitution of a choline by a H-atom.
>
> First, I did conserve charge.
> Second, I did introduce reasonable non-bonded and bonded interaction  
> parameters for the new H-atom. The non-bonded interaction parameters  
> were similar to those suggested by the mono-anionic phosphate group  
> on a threonine or serine.
>
> I guess you will agree force fields are often set up that entire  
> functional groups from one molecule can be transferred to others.  
> For example, one can use the same head group for both POPC and DPPC,  
> or conversely, one can use different types of hydrocarbon chains for  
> the same head group, from 12 carbons to 20 carbons, as has often  
> been done. The only parameters that might change in getting POPA  
> from POPC are near the H-atom itself, and those are the ones that I  
> had posted earlier, just to see if anyone could notice a mistake.
>
> Similar methods have been used in literature earlier, except that a  
> DFT calculation was made for the mono-anionic phosphate group to get  
> new charges. The DFT did reveal that charges on DOPA were similar to  
> DOPC.
>
> The main issue I have is that I get a somewhat skewed phosphate  
> group that leads to unfavorable positions for the oxygen atoms on  
> phosphate. I am guessing that this is because of the bonded- 
> interactions of the new H-atom.
>
>
> On Mon, May 5, 2008 at 3:10 PM, Mark Abraham  
> <Mark.Abraham at anu.edu.au> wrote:
> himanshu khandelia wrote:
> Hi,
>
> I am trying to run a simulation of a POPC bilayer mixed with some
> mono-anionic Phosphatidic acid (POPA) , where the choline group is
> replaced by a hydrogen atom. However, the energy of my simulation box
> diverges, and I am trying to fix the problem. I also tried running a
> simulation of PA solvated in water and a single sodium ion, but even
> that does not work. I will try to provide as much detail as possible,
> I hope someone can help point out some obvious error which I have not
> been able to debug over 3 days. In the simulation of a single PA
> molecule in water, MDRUN keeps complaining that the distance between
> atoms H1 and O4 is very high (> 4 nm or so). The problem probably lies
> in my topology, possibly in the bonded interactions?
>
> Merely replacing a functional group with a hydrogen doesn't make for  
> a sensible model physics. First, you probably didn't conserve  
> charge, and second the parameters don't necessarily make sense for a  
> particle of mass 1 rather than mass 12 (plus secondary effect of  
> substituent group), and third there's no way to fix both the  
> foregoing and the other issues.
>
> You need at least to find a proper model of POPA and to implement  
> it, or if need be, develop one yourself. Search the wiki for  
> Parameterization to get a start on the latter, but it is an expert  
> topic.
>
> Mark
>
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> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen _______________________________________________
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