[gmx-users] dimerization problem

[Tsjerk Wassenaar]

Hi Prasun,

As a side-note to the replies of Justin and Florian, why not take the
following approach?:

1. run pdb2gmx on the monomer, giving structure and topology for one unit
(2. energy minimize in vacuum)
3. use editconf to make a transformed copy of the monomer
-- now, you know for sure that both are topologically identical --
4. concatenate the two chains; if it's pdb format just grep all ATOM
records from both files into a new file
5. modify Protein  1 to Protein  2 under [ molecules ] in the topology
6. setup a box and solvate and continue as usual

Hope it helps,

Tsjerk

On Thu, Jul 31, 2008 at 2:24 PM, Florian Haberl
<Florian.Haberl at chemie.uni-erlangen.de> wrote:
> Hi,
>
> On Thursday, 31. July 2008, prasun kumar wrote:
>> Dear user,
>> I want to check the dimerization of a peptide chain having 227 residues.I
>> am doing the following steps:
>>
>> 1. First i transformed the given peptide by 20 angstrom by
>>    modifying corresponding pdb file and save it as
>>    f1.pdb(say),original file given was 'f.pdb'(say)
>>
>> 2 .Now i run the pdb2gmx command for both the proteins.
>>
>> 3 add the two files and remove the END of one of the file(i
>>    mean   to say i remove the END from the middle).
>>
>> 4. Now run the EDITCONF command
>>
>> 5 Modify the topology file in the molecules section by
>>    replacing 1 by2.
>>
>> 6 run the grompp command and mdrun for energy
>>    minimization for 2000 steps.
>>
>> 7 again run grompp for positional restrained dynamics
>>
>> till here every thing work
>>
>> but when i tried to run mdrun its telling your protein is not minimizd
>> properly.
>>
>> after  this I tried another method by modifying opology file in the
>> following way
>>
>> I added one proteins topology file in the another one by adding line
>> INCLUDE f1_top1.top(topology file name)
>>
>> again its working till grompp(pr)
>> now when i am trying to run mdrun its givin following error
>>
>> Found a second defaults directive, file
>> "/usr/share/gromacs/top/ffG43a1.itp", line 6
>>
>> What to do?
>>
>> I am not getting any other way.Please help me.
>>
>> Thanx in advance
>> Regards
>>
>> PRASUN (ASHOKA)
>
> Have you checked your structure (missing residues and so on ..), can you
> simulate one monomer without problems?
>
> In principle it should work with the first approach, but it is. (often)
> neccessary to start the simulation with position restraints to get a valid
> structure for a free MD simulation.
>
> See the wiki for the normal simulation protocol (
> http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation )
>
>
>
> greetings,
>
> Florian
>
> --
> -------------------------------------------------------------------------------
>  Florian Haberl
>  Computer-Chemie-Centrum
>  Universitaet Erlangen/ Nuernberg
>  Naegelsbachstr 25
>  D-91052 Erlangen
>  Telephone:     +49(0) − 9131 − 85 26573
>  Mailto: florian.haberl AT chemie.uni-erlangen.de
> -------------------------------------------------------------------------------
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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