[gmx-users] provide opt way to perform simulation for protein and peptide -reg

venkatesh s svenkateshbioinformatics at gmail.com
Fri Sep 28 16:07:53 CEST 2012

Respected gromacs Users,
                                         i want perform stimulation for
protein + peptide (in water medium only not membrane protein)
1. Can i use the Docked conformation (better conformation both protein +
peptide make it as one file .pdb ) for perform simulation
2. Other than that manually edit the coordinate file  after TER or END
insert peptide amino acid (my peptide having a 5 amino acid )
Please Provide which one the is best even other than two

Thanking You


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