[gmx-users] splitting chains

[Tsjerk Wassenaar]

Ozge,

We are, at least I am, getting the impression that you refuse to try
to think for your self. This makes trying to help you very
unsatisfactory. We are not here to do your homework.

Ok, that been said, I'll make it brief. You shouldn't need to edit the
specbond.dat (in the gromacs topology/data directory). Issuing -merge
with pdb2gmx will make it recognize multiple chains as one molecule
allowing interchain bonds.

Next time, please be more prepared, at least suggesting that you've
tried some things (reading?) to find a solution to your problem and
give more thoughts about phrasing your question (english, logic,
information required).

Tsjerk

On 3/30/07, özge kül <ozgekul8233 at yahoo.com> wrote:
> Hi Andrea,
>
> This is my .top file
> more 1ppbfree.top
> ;
> ;       File '1ppbfree.top' was generated
> ;       By user: ozge (502)
> ;       On host: druggrid
> ;       At date: Thu Mar 15 23:17:25 2007
> ;
> ;       This is your topology file
> ;       ALPHA-THROMBIN (E.C.3.4.21.5) COMPLEX W
> ;
> ; Include forcefield parameters
> #include "ffG43a1.itp"
>
> ; Include chain topologies
> #include "1ppbfree_H.itp"
> #include "1ppbfree_L.itp"
>
> ; Include water topology
> #include "spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>
> ; Include generic topology for ions
> #include "ions.itp"
>
> [ system ]
> ; Name
> ALPHA-THROMBIN (E.C.3.4.21.5) COMPLEX W in water
>
> [ molecules ]
> ; Compound        #mols
> Protein_H           1
> Protein_L           1
> SOL              8695
>
>
> Thank you very much again and again...
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623