[gmx-users] dimerization problem

prasun kumar prasun30 at gmail.com
Thu Jul 31 14:11:23 CEST 2008

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

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

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