[gmx-users] pdb2gmx for non-proteins

[Anton Feenstra]

Christoph Freudenberger wrote:
> Hi there,
> 
> I'm thinking about how to generate the top's for tripodal
> scaffold-molecules bearing different substituents:
> 
>     R1
>       \
>        Scaf--R3
>       /
>     R2
> 
> The scaffold is an aryl-ring and R1-3 should be arbituary
> substiutents.
> I wonder if it is possible to add rtp-entries for Scaf and
> the R's and let pdb2gmx do the job.
> Is pdb2gmx able to handle non-chain-like molecules?

No and yes. Initially, bonds are only made between consecutive
residues (as I describe below). Then, there are the 'special
bonds' from the file 'specbonds.dat', where additional bonds
are defined. So, you can have bonds genereated 'sequentially'
e.g. between R1, Scaf and R2, and have a 'specbond' between
Scaf and R3. Note, that the sequential bonds are always made,
they are defined in the .rtp, but the specbonds are only
made if a distance criterium is met (the reference distance
from 'specbond.dat' +/- 10%). You will still need an .rtp
entry for R3, of course. (Compare e.g. Cys-Heme and Cys-Cys
bonds.)

> How are the links recognized? Automaticly (e.g. by distance)
> or do I have to define them?

Automatically, from the definitions in the .rtp by making bonds
to, e.g., atom '-C' ('C' atom in previous residue), or '+N' ('N'
atom in next residue). Distances are not checked here.

> Is it vital to have the atoms in the same sequence in the
> pdb and the rtp?

No, pdb2gmx will sort your .pdb atoms into the .rtp order.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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