[gmx-users] dimerization problem

[Florian Haberl]

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

-- 
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 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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