[gmx-users] how to stop duplicate atoms from being deleted

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 23 20:07:31 CEST 2009



Jennifer Williams wrote:
> 
> Thanks again for the help. I?ve given it a go but am not overly 
> confident or exactly sure how I would translate this method to my system.
> 
> This is because rather than having a chain with a well defined start and 
> finish I have a giant covalent structure (like a web) where each silicon 
> is tetrahedrally bound to oxygen (as in quartz).
> 
>          O?
>          |
>       ?O-Si-O ?
>          |
>          O?
> 
> Here I describe my efforts so far.
> 
> I have defined a monomer (my internal unit) as an SiO4 tetrahedra.   
> Therefore each monomer would have to form 4 bonds with other monomers. I 
> have defined my internal residue like this:
> 
> ; Internal residue
> [ MCM_I ]
>  [ atoms ]
>    SI    SI    1.280     1
>    O1    O1   -0.640     1
>    O2    O2   -0.640     1
>    O3    O3   -0.640     1
>    O4    O4   -0.640     1
> 
>   [ bonds ]
>     SI    O1
>     SI    O2
>     SI    O3
>     SI    O4
>     O1   -SI
>     O2   -SI
>     O3   +SI
>     O4   +SI
> 
> As an aside-This means that each residue is not neutral as the charges 
> cancel out over the entire molecule and not over a single residue-I am 
> not sure of the implications of this.
> 
> To complicate matters, in my structure not all of the oxygens are bonded 
> oxygens (i.e where each O is bonded to 2 silicons, some of the oxygens 
> terminate in hydroxyl groups). This means that I have will have 3 types 
> of terminal/starting chain
> 
> 1. Si, O, O, OH
> 2. SI, O, OH, OH
> 3. SI, OH, OH, OH (the group which really does terminate)
> 
> Here are my terminal and starting residues:
> 
> 
> ; terminal residue 1 (3OH groups)
> [ MCM_T1 ]
>  [ atoms ]
>    SI    SI     1.280     1
>   OH1    OH1   -0.502     1
>    H1    H1     0.206     1
>   OH2    OH2   -0.502     1
>    H2    H2     0.206     1
>   OH3    OH3   -0.502     1
>    H3    H3     0.206     1
>    O4    O4    -0.640     1
> 
>   [ bonds ]
>     SI   OH1
>     SI   OH2
>     SI   OH3
>     SI    O4
>     OH1   H1
>     OH2   H2
>     OH3   H3
>      O4  -SI
> 
> ; terminal residue 2 (2 OH groups)
> [ MCM_T2 ]
>  [ atoms ]
>   SI    SI     1.280     1
>   OH1   OH1    -0.502     1
>    H1    H1     0.206     1
>   OH2   OH2    -0.502     1
>    H2    H2     0.206     1
>    O3    O3    -0.640     1
>    O4    O4    -0.640     1
> 
>   [ bonds ]
>     SI   OH1
>     SI   OH2
>     SI    O3
>     SI    O4
>     OH1   H1
>     OH2   H2
>      O3  -SI
>      O4  -SI
> 
> 
> ; terminal residue 3 (1 OH group)
> [ MCM_T3 ]
>  [ atoms ]
>   SI   SI     1.280     1
>   OH1   OH1    -0.502     1
>    H1    H1     0.206     1
>    O2    O2    -0.640     1
>    O3    O3    -0.640     1
>    O4    O4    -0.640     1
> 
>   [ bonds ]
>     SI   OH1
>     SI    O2
>     SI    O3
>     SI    O4
>     OH1    H1
>      O2  -SI
>      O3  -SI
>      O4  -SI
> 
> As each of these groups could equally be starting groups-I have defined 
> them as such by changing the minus sign to a plus
> 
> ; starting residue 1
> [ MCM_S1 ]
>  [ atoms ]
>   SI    SI    1.280     1
>   OH1    OH1   -0.502     1
>    H1    H1     0.206     1
>   OH2    OH2   -0.502     1
>    H2    H2     0.206     1
>   OH3    OH3   -0.502     1
>    H3    H3     0.206     1
>    O4    O4    -0.640     1
> 
>   [ bonds ]
>     SI   OH1
>     SI   OH2
>     SI   OH3
>     SI    O4
>      O4  +SI
> 
> ; starting residue 2
> [ MCM_T2 ]
>  [ atoms ]
>   SI    SI     1.280     1
>   OH1   OH1    -0.502     1
>    H1    H1     0.206     1
>   OH2   OH2    -0.502     1
>    H2    H2     0.206     1
>    O3    O3    -0.640     1
>    O4    O4    -0.640     1
> 
>   [ bonds ]
>     SI   OH1
>     SI   OH2
>     SI    O3
>     SI    O4
>      O3  +SI
>      O4  +SI
> 
> 
> ; starting residue 3
> [ MCM_T3 ]
>  [ atoms ]
>   SI   SI     1.280     1
>   OH1   OH1    -0.502     1
>    H1    H1     0.206     1
>    O2    O2    -0.640     1
>    O3    O3    -0.640     1
>    O4    O4    -0.640     1
> 
>   [ bonds ]
>     SI   OH1
>     SI    O2
>     SI    O3
>     SI    O4
>      O2  +SI
>      O3  +SI
>      O4  +SI
> 
> 
> There are a few problems with this:
> 
> 1.    I don?t know how to go about splitting my large .pdb file into 
> monomers. At the moment it is ordered by atomtype VMD doesn?t recognise 
> my self- defined SiO2 tetrahedra as monomers so I can?t sort using that. 
> There is no way I can do this manually by looking at the coordinates.
> 
> 2.    Looking at the terminal residue 1 for example, I have defined the 
> only non-bonded oxygen as O4-however it could equally be O1, O2 or 
> O3-this leads to a number of possible combinations of my terminal and 
> internal residues.
> 
> 3.    There is in fact no such thing as a terminal residue (except in 
> the case of Terminal residue 1 which is rare). It is more common to have 
> a 2 OH groups on a silicon meaning the other oxygens bond to further 
> residues.
> 
> I can see how this method works nicely for a chain but having a four 
> coordinate system really complicates things! I have run a very simple 
> pdb file using pdb2gmx, the new .rtp file above and a handwritten .pdb 
> file with 2 monomers.
> The result is that pdb2gmx  is creating extra bonds between the Silicon 
> of one monomer and the oxygen of the next meaning I am getting a 
> 5-coordinate Silicon.
> 
> Pdb2gmx doesn?t seem to be able to distinguish based on bond distances 
> which oxygens belong to which monomer. The only way I can see past this 
> is a more elaborate naming system which would introduce yet more 
> combinations.
> 
> So I?m throwing this out as a last resort before I give up. Has anyone 
> had any success using this method for a similar system? Quartz?

I can see how this rapidly becomes difficult :)  I don't believe that pdb2gmx 
can handle such "multi-directional" bonding, since the residues that are 
connected are not necessarily numerically sequential.

There is, however, another alternative that might work.  The specbond.dat file 
allows for bizarre connections, provided the atoms are within 10% of a defined 
distance cutoff.  You probably wouldn't even have to worry about renumbering or 
reorganizing your structure.

I would suggest generating a small test case - like a 3x3 grid of tetrahedral 
centers, which should encompass all the different types of units (interior, 
multiple -OH instead of -O-).

Don't give up, this can surely be accomplished :)  Please report back with any 
problems or successes.  If we can work this out, it would be a fantastic example 
for the wiki to help future users.

-Justin

> 
> Sorry for my rambling
> 
> Jenny

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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