[gmx-users] pdb2gmx for non-proteins

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Thu Apr 17 10:07:01 CEST 2003

Hi Anton,

Anton Feenstra wrote:
> 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.

If understood that correctly, pdb2gmx would look for something
like this:

But of course my system goes:

I suppose this is only possible by defining all three bonds
via specbonds.dat.
I'll give it a try.

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785

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