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
If your system isn't minimized properly, changing the format of the topology
won't fix it. You've probably got some type of steric clash that can't be
resolved. Did energy minimization cut off at 2000 steps, or did it complete
before that? You could always try running more EM if it ended at 2000.
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?
Consult the wiki, the answer is there:
http://wiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
-Justin
I am not getting any other way.Please help me.
Thanx in advance
Regards
PRASUN (ASHOKA)
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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