<div dir="ltr">Dear user,<br>I want to check the dimerization of a peptide chain having 227 residues.I am doing the following steps:<br><br>1. First i transformed the given peptide by 20 angstrom by <br> modifying corresponding pdb file and save it as <br>
f1.pdb(say),original file given was 'f.pdb'(say)<br><br>2 .Now i run the pdb2gmx command for both the proteins.<br><br>3 add the two files and remove the END of one of the file(i <br> mean to say i remove the END from the middle).<br>
<br>4. Now run the EDITCONF command <br><br>5 Modify the topology file in the molecules section by <br> replacing 1 by2.<br><br>6 run the grompp command and mdrun for energy <br> minimization for 2000 steps.<br><br>7 again run grompp for positional restrained dynamics<br>
<br>till here every thing work <br><br>but when i tried to run mdrun its telling your protein is not minimizd properly.<br><br>after this I tried another method by modifying opology file in the following way <br><br>I added one proteins topology file in the another one by adding line INCLUDE f1_top1.top(topology file name)<br>
<br>again its working till grompp(pr) <br>now when i am trying to run mdrun its givin following error<br><br>Found a second defaults directive, file "/usr/share/gromacs/top/ffG43a1.itp", line 6<br><br clear="all">
What to do?<br><br>I am not getting any other way.Please help me.<br><br>Thanx in advance<br>Regards<br><br>PRASUN (ASHOKA)<br>
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