Re: [gmx-users] dimerization problem

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 b

Re: [gmx-users] dimerization problem

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.p

Re: [gmx-users] dimerization problem

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

[gmx-users] dimerization problem

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 pdb