[gmx-users] pdb2gmx for non-proteins

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Thu Apr 17 11:57:01 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.)
Ok, I understand the concept (more or less) now. I think I could
gain some more flexibilty if I use specbonds (e.g. if two or three
R's are equal).
Unforunatly the fileformat is not documented (or I missed it).
Let's see if I guessed it correctly:

CYS     SG      1       CYS     SG      1       0.2     CYS2    CYS2
CYS     SG      1       HEME    FE      2       0.25    CYS2    HEME
CYS     SG      1       HEME    CAB     1       0.2     CYS2    HEME
CYS     SG      1       HEME    CAC     1       0.2     CYS2    HEME
HIS     NE2     1       HEME    FE      1       0.2     HIS1    HEME
res     atom    ?       res     atom    ?       cut       resnames
name    name            name    name            off          in
in                      in                                   rtp
pdb                     pdb

Would you please confirm (or correct) my interpretation and tell me what ? is.

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

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